From 88931b2fafc06231b834ff4fdba45f088294c148 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 25 Apr 2024 14:01:23 +0200 Subject: [PATCH 01/32] Replicate circRNA discovery for benchmarking --- assets/schema_input.json | 6 ++++++ nextflow.config | 1 + workflows/circrna/main.nf | 36 +++++++++++++++++++++++++++++++++--- 3 files changed, 40 insertions(+), 3 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 7e9257a0..d79fa807 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -27,6 +27,12 @@ "pattern": "^\\S+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, + "benchmarking": { + "type": "boolean", + "default": false, + "errorMessage": "Benchmarking must be a boolean value", + "meta": ["benchmarking"] + }, "strandedness": { "type": "string", "enum": ["unstranded", "forward", "reverse", "auto"], diff --git a/nextflow.config b/nextflow.config index e2c6308d..d638aa58 100644 --- a/nextflow.config +++ b/nextflow.config @@ -22,6 +22,7 @@ params { duplicates_fun = 'mean' exon_boundary = 200 save_intermediates = false + benchmarking = false // References genome = null diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index a16fb752..532cc82c 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -29,6 +29,7 @@ include { validateInputSamplesheet } from '../../subworkflows/local/util include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { PREPARE_GENOME } from '../../subworkflows/local/prepare_genome' include { CIRCRNA_DISCOVERY } from '../../subworkflows/local/circrna_discovery' +include { CIRCRNA_DISCOVERY as CIRCRNA_DISCOVERY_BENCHMARKING } from '../../subworkflows/local/circrna_discovery_benchmarking' include { QUANTIFICATION } from '../../subworkflows/local/quantification' include { MIRNA_PREDICTION } from '../../subworkflows/local/mirna_prediction' include { STATISTICAL_TESTS } from '../../subworkflows/local/statistical_tests' @@ -134,8 +135,13 @@ workflow CIRCRNA { // 2. circRNA Discovery // + FASTQC_TRIMGALORE.out.reads.branch{ + real: !it[0].benchmarking + benchmarking: it[0].benchmarking + }.set{ ch_reads } + CIRCRNA_DISCOVERY( - FASTQC_TRIMGALORE.out.reads, + ch_reads.real, ch_fasta, ch_gtf, bowtie_index, @@ -155,7 +161,31 @@ workflow CIRCRNA { ch_versions = ch_versions.mix(CIRCRNA_DISCOVERY.out.versions) // - // 3. Quantification + // 3. Benchmarking + // + + if (params.benchmarking) { + CIRCRNA_DISCOVERY_BENCHMARKING( + ch_reads.benchmarking, + ch_fasta, + ch_gtf, + bowtie_index, + bowtie2_index, + bwa_index, + chromosomes, + hisat2_index, + segemehl_index, + star_index, + params.bsj_reads, + params.tool_filter, + params.duplicates_fun, + params.exon_boundary + ) + ch_versions = ch_versions.mix(CIRCRNA_DISCOVERY_BENCHMARKING.out.versions) + } + + // + // 4. Quantification // QUANTIFICATION( @@ -173,7 +203,7 @@ workflow CIRCRNA { ch_versions = ch_versions.mix(QUANTIFICATION.out.versions) // - // 4. miRNA prediction + // 5. miRNA prediction // if (params.mature) { MIRNA_PREDICTION( From 56d6bd50f1152ffbdba5ff7bc9c742e88b308eed Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 25 Apr 2024 17:10:07 +0200 Subject: [PATCH 02/32] Implement Jaccard calculation --- conf/modules.config | 21 ++++++- modules.json | 10 ++++ .../nf-core/bedtools/jaccard/environment.yml | 7 +++ modules/nf-core/bedtools/jaccard/main.nf | 49 ++++++++++++++++ modules/nf-core/bedtools/jaccard/meta.yml | 57 +++++++++++++++++++ .../nf-core/bedtools/merge/environment.yml | 7 +++ modules/nf-core/bedtools/merge/main.nf | 47 +++++++++++++++ modules/nf-core/bedtools/merge/meta.yml | 45 +++++++++++++++ .../nf-core/bedtools/merge/tests/main.nf.test | 34 +++++++++++ .../bedtools/merge/tests/main.nf.test.snap | 35 ++++++++++++ .../bedtools/merge/tests/nextflow.config | 7 +++ modules/nf-core/bedtools/merge/tests/tags.yml | 2 + nextflow_schema.json | 28 +++++++-- subworkflows/local/benchmarking.nf | 38 +++++++++++++ subworkflows/local/circrna_discovery.nf | 2 +- workflows/circrna/main.nf | 9 ++- 16 files changed, 391 insertions(+), 7 deletions(-) create mode 100644 modules/nf-core/bedtools/jaccard/environment.yml create mode 100644 modules/nf-core/bedtools/jaccard/main.nf create mode 100644 modules/nf-core/bedtools/jaccard/meta.yml create mode 100644 modules/nf-core/bedtools/merge/environment.yml create mode 100644 modules/nf-core/bedtools/merge/main.nf create mode 100644 modules/nf-core/bedtools/merge/meta.yml create mode 100644 modules/nf-core/bedtools/merge/tests/main.nf.test create mode 100644 modules/nf-core/bedtools/merge/tests/main.nf.test.snap create mode 100644 modules/nf-core/bedtools/merge/tests/nextflow.config create mode 100644 modules/nf-core/bedtools/merge/tests/tags.yml create mode 100644 subworkflows/local/benchmarking.nf diff --git a/conf/modules.config b/conf/modules.config index 369b900d..20c77055 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -607,10 +607,29 @@ process { path: { "${params.outdir}/circrna_discovery/${meta.tool}/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - pattern: "*.backspliced.fa" + pattern: "*.fasta" ] } + withName: COUNTS_COMBINED { + ext.when = { params.module.split(',').contains('circrna_discovery') } + } + + withName: COUNTS_TO_BED { + ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\" }'" + ext.suffix = "bed" + } + + withName: UNIQUE_REGIONS { + ext.args = "-k 1,1 -k2,2n -k3,3n -u" + ext.suffix = "unique.bed" + } + + withName: '.*:BENCHMARKING:SORT' { + ext.args = "-k 1,1 -k2,2n -k3,3n -u" + ext.suffix = "combined.bed" + } + withName: COMBINE_TRANSCRIPTOME_GTFS { ext.args = "-k 1,1 -k4,4n -k5,5n" ext.suffix = "gtf" diff --git a/modules.json b/modules.json index 3792423c..1b54424a 100644 --- a/modules.json +++ b/modules.json @@ -15,6 +15,16 @@ "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", "installed_by": ["modules"] }, + "bedtools/jaccard": { + "branch": "master", + "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "installed_by": ["modules"] + }, + "bedtools/merge": { + "branch": "master", + "git_sha": "a5377837fe9013bde89de8689829e83e84086536", + "installed_by": ["modules"] + }, "bedtools/sort": { "branch": "master", "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", diff --git a/modules/nf-core/bedtools/jaccard/environment.yml b/modules/nf-core/bedtools/jaccard/environment.yml new file mode 100644 index 00000000..f0f2a38f --- /dev/null +++ b/modules/nf-core/bedtools/jaccard/environment.yml @@ -0,0 +1,7 @@ +name: bedtools_jaccard +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/jaccard/main.nf b/modules/nf-core/bedtools/jaccard/main.nf new file mode 100644 index 00000000..32a41210 --- /dev/null +++ b/modules/nf-core/bedtools/jaccard/main.nf @@ -0,0 +1,49 @@ +process BEDTOOLS_JACCARD { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" + + input: + tuple val(meta), path(input_a), path(input_b) + tuple val(meta2), path(genome_file) + + output: + tuple val(meta), path("*.tsv"), emit: tsv + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def genome = genome_file ? "-g ${genome_file}" : "" + """ + bedtools jaccard \\ + -a ${input_a} \\ + -b ${input_b} \\ + ${genome} \\ + ${args} \\ + > ${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/bedtools/jaccard/meta.yml b/modules/nf-core/bedtools/jaccard/meta.yml new file mode 100644 index 00000000..2b542284 --- /dev/null +++ b/modules/nf-core/bedtools/jaccard/meta.yml @@ -0,0 +1,57 @@ +name: "bedtools_jaccard" +description: Calculate Jaccard statistic b/w two feature files. +keywords: + - vcf + - gff + - bed + - jaccard + - intersection + - union + - statistics +tools: + - "bedtools": + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_a: + type: file + description: VCF,GFF or BED file to use with the `-a` option + pattern: "*.{vcf,vcf.gz,bed,bed.gz,gff}" + - input_b: + type: file + description: VCF,GFF or BED file to use with the `-b` option + pattern: "*.{vcf,vcf.gz,bed,bed.gz,gff}" + - meta2: + type: map + description: | + Groovy Map containing genome file information + e.g. [ id:'test', single_end:false ] + - genome_file: + type: file + description: A file containing all the contigs of the genome used to create the input files + pattern: "*.{txt,sizes,fai}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - tsv: + type: file + description: TSV file containing the results + pattern: "*.tsv" +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/modules/nf-core/bedtools/merge/environment.yml b/modules/nf-core/bedtools/merge/environment.yml new file mode 100644 index 00000000..99707878 --- /dev/null +++ b/modules/nf-core/bedtools/merge/environment.yml @@ -0,0 +1,7 @@ +name: bedtools_merge +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf new file mode 100644 index 00000000..5310647d --- /dev/null +++ b/modules/nf-core/bedtools/merge/main.nf @@ -0,0 +1,47 @@ +process BEDTOOLS_MERGE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" + + input: + tuple val(meta), path(bed) + + output: + tuple val(meta), path('*.bed'), emit: bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if ("$bed" == "${prefix}.bed") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + bedtools \\ + merge \\ + -i $bed \\ + $args \\ + > ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/bedtools/merge/meta.yml b/modules/nf-core/bedtools/merge/meta.yml new file mode 100644 index 00000000..d7463e3d --- /dev/null +++ b/modules/nf-core/bedtools/merge/meta.yml @@ -0,0 +1,45 @@ +name: bedtools_merge +description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features. +keywords: + - bed + - merge + - bedtools + - overlapped bed +tools: + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Overlapped bed file with combined features + pattern: "*.{bed}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@edmundmiller" + - "@sruthipsuresh" + - "@drpatelh" +maintainers: + - "@edmundmiller" + - "@sruthipsuresh" + - "@drpatelh" diff --git a/modules/nf-core/bedtools/merge/tests/main.nf.test b/modules/nf-core/bedtools/merge/tests/main.nf.test new file mode 100644 index 00000000..95dba8e5 --- /dev/null +++ b/modules/nf-core/bedtools/merge/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process BEDTOOLS_MERGE" + script "../main.nf" + config "./nextflow.config" + process "BEDTOOLS_MERGE" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/merge" + + test("test_bedtools_merge") { + + when { + process { + """ + input[0] = [ [ id:'test'], + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/merge/tests/main.nf.test.snap b/modules/nf-core/bedtools/merge/tests/main.nf.test.snap new file mode 100644 index 00000000..ee6c4e63 --- /dev/null +++ b/modules/nf-core/bedtools/merge/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test_bedtools_merge": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,0cf6ed2b6f470cd44a247da74ca4fe4e" + ] + ], + "1": [ + "versions.yml:md5,2d134badb4cd1e4e903696c7967f28d6" + ], + "bed": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,0cf6ed2b6f470cd44a247da74ca4fe4e" + ] + ], + "versions": [ + "versions.yml:md5,2d134badb4cd1e4e903696c7967f28d6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T17:07:09.721153" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/merge/tests/nextflow.config b/modules/nf-core/bedtools/merge/tests/nextflow.config new file mode 100644 index 00000000..16444e98 --- /dev/null +++ b/modules/nf-core/bedtools/merge/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: BEDTOOLS_MERGE { + ext.prefix = { "${meta.id}_out" } + } + +} diff --git a/modules/nf-core/bedtools/merge/tests/tags.yml b/modules/nf-core/bedtools/merge/tests/tags.yml new file mode 100644 index 00000000..60c8cad1 --- /dev/null +++ b/modules/nf-core/bedtools/merge/tests/tags.yml @@ -0,0 +1,2 @@ +bedtools/merge: + - "modules/nf-core/bedtools/merge/**" diff --git a/nextflow_schema.json b/nextflow_schema.json index c1b06562..91ff3329 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,7 +10,10 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": ["input", "outdir"], + "required": [ + "input", + "outdir" + ], "properties": { "input": { "type": "string", @@ -91,7 +94,10 @@ "fa_icon": "fas fa-copy", "description": "Aggregate function to apply to duplicate circRNAs when more than one quantification tool has been selected. Options: max, mean", "default": "mean", - "enum": ["mean", "max"] + "enum": [ + "mean", + "max" + ] }, "save_intermediates": { "type": "boolean", @@ -104,6 +110,13 @@ "description": "Specify the distance at which the annotation script decides if a candidate is a circRNA or EI-circRNA.", "help_text": "During annotation, if one of the start or end position of a circular candidate imperfectly overlaps an exon boundary, the script will consider positions within 'exon_boundary' (default 200bp) to be an exonic circRNA. If they fall outside of this range, the candidate is assumed to be an exonic-intronic circRNA, and the entire underlying sequence is taken for miRNA analysis, as opposed to just the exonic sequences for canonical exonic circRNAs. ", "default": 200 + }, + "benchmarking": { + "type": "boolean", + "description": "Run the pipeline in benchmarking mode.", + "default": false, + "fa_icon": "fas fa-chart-line", + "help_text": "This enables parallel analysis of polyA-enriched data with the same circRNA quantification tools to compare performance." } } }, @@ -453,7 +466,14 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ], "hidden": true }, "email": { @@ -578,4 +598,4 @@ "$ref": "#/definitions/generic_options" } ] -} +} \ No newline at end of file diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf new file mode 100644 index 00000000..fcabebe4 --- /dev/null +++ b/subworkflows/local/benchmarking.nf @@ -0,0 +1,38 @@ +include { GNU_SORT as SORT } from '../../modules/nf-core/gnu/sort' +include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge' +include { BEDTOOLS_JACCARD } from '../../modules/nf-core/bedtools/jaccard' + +workflow BENCHMARKING { + + take: + ch_real_bed + ch_benchmarking_bed + + main: + + ch_versions = Channel.empty() + + ch_all = ch_real_bed.mix(ch_benchmarking_bed) + .map{ meta, bed -> [[id: meta.tool + "_" + (meta.benchmarking ? "benchmarking" : "real"), + tool: meta.tool, + benchmarking: meta.benchmarking], bed]} + .groupTuple() + + SORT(ch_all) + BEDTOOLS_MERGE(SORT.out.sorted).bed.branch{ meta, bed -> + real: !meta.benchmarking + benchmarking: meta.benchmarking + }.set { ch_merged } + + ch_joined = ch_merged.real.map{ meta, bed -> [[id: meta.tool], bed]} + .join(ch_merged.benchmarking.map{ meta, bed -> [[id: meta.tool], bed]}) + + ch_jaccard = BEDTOOLS_JACCARD(ch_joined, [[], []]).tsv + + ch_versions = ch_versions.mix(SORT.out.versions) + ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) + ch_versions = ch_versions.mix(BEDTOOLS_JACCARD.out.versions) + + emit: + versions = ch_versions // channel: [ versions.yml ] +} diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 2a163ce7..c4218ca0 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -155,7 +155,7 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) emit: - circrna_bed12 = ANNOTATION.out.merged_bed + tool_bed = ANNOTATION.out.merged_bed fasta = ADD_BACKSPLICE.out.output annotation_bed = ANNOTATION.out.bed annotation_gtf = ANNOTATION.out.gtf diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 532cc82c..23df0513 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -29,7 +29,8 @@ include { validateInputSamplesheet } from '../../subworkflows/local/util include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { PREPARE_GENOME } from '../../subworkflows/local/prepare_genome' include { CIRCRNA_DISCOVERY } from '../../subworkflows/local/circrna_discovery' -include { CIRCRNA_DISCOVERY as CIRCRNA_DISCOVERY_BENCHMARKING } from '../../subworkflows/local/circrna_discovery_benchmarking' +include { CIRCRNA_DISCOVERY as CIRCRNA_DISCOVERY_BENCHMARKING } from '../../subworkflows/local/circrna_discovery' +include { BENCHMARKING } from '../../subworkflows/local/benchmarking' include { QUANTIFICATION } from '../../subworkflows/local/quantification' include { MIRNA_PREDICTION } from '../../subworkflows/local/mirna_prediction' include { STATISTICAL_TESTS } from '../../subworkflows/local/statistical_tests' @@ -181,6 +182,12 @@ workflow CIRCRNA { params.duplicates_fun, params.exon_boundary ) + + BENCHMARKING( + CIRCRNA_DISCOVERY.out.tool_bed, + CIRCRNA_DISCOVERY_BENCHMARKING.out.tool_bed + ) + ch_versions = ch_versions.mix(CIRCRNA_DISCOVERY_BENCHMARKING.out.versions) } From 31dc5e8342a5b34a5589dc98e2b0cdf8d079aa86 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 25 Apr 2024 17:54:48 +0200 Subject: [PATCH 03/32] Implement jaccard file collection --- subworkflows/local/benchmarking.nf | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index fcabebe4..95597227 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -29,6 +29,14 @@ workflow BENCHMARKING { ch_jaccard = BEDTOOLS_JACCARD(ch_joined, [[], []]).tsv + ch_stats = ch_jaccard.splitCsv(header: true, sep: "\t") + .map{ meta, values -> [meta.id, values.intersection, values.union, values.jaccard, values.n_intersections]} + .collectFile( newLine: true, + storeDir: params.outdir, + seed: "tool\tintersection\tunion\tjaccard\tn_intersections") { + row -> ["jaccard.tsv", row.join("\t")] + } + ch_versions = ch_versions.mix(SORT.out.versions) ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) ch_versions = ch_versions.mix(BEDTOOLS_JACCARD.out.versions) From 650480c08d712db98c5116a466e34185b4a96891 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 25 Apr 2024 19:29:56 +0200 Subject: [PATCH 04/32] Add benchmarking multiqc configuration --- assets/multiqc_config.yml | 7 ++- modules/local/benchmarking/multiqc/main.nf | 18 ++++++++ .../multiqc/templates/benchmarking.py | 46 +++++++++++++++++++ subworkflows/local/benchmarking.nf | 13 ++++-- workflows/circrna/main.nf | 2 + 5 files changed, 80 insertions(+), 6 deletions(-) create mode 100644 modules/local/benchmarking/multiqc/main.nf create mode 100644 modules/local/benchmarking/multiqc/templates/benchmarking.py diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 570f6c0d..34963d4a 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -5,10 +5,13 @@ report_comment: > report_section_order: "nf-core-circrna-methods-description": order: -1000 - software_versions: + benchmarking: order: -1001 - "nf-core-circrna-summary": + software_versions: order: -1002 + "nf-core-circrna-summary": + order: -1003 + export_plots: true diff --git a/modules/local/benchmarking/multiqc/main.nf b/modules/local/benchmarking/multiqc/main.nf new file mode 100644 index 00000000..5e991ff1 --- /dev/null +++ b/modules/local/benchmarking/multiqc/main.nf @@ -0,0 +1,18 @@ +process BENCHMARKING_MULTIQC { + label "process_single" + + conda "bioconda::pandas=1.5.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'biocontainers/pandas:1.5.2' }" + + input: + path(jaccard) + + output: + path("benchmarking_mqc.json"), emit: report + path("versions.yml") , emit: versions + + script: + template "benchmarking.py" +} \ No newline at end of file diff --git a/modules/local/benchmarking/multiqc/templates/benchmarking.py b/modules/local/benchmarking/multiqc/templates/benchmarking.py new file mode 100644 index 00000000..86386873 --- /dev/null +++ b/modules/local/benchmarking/multiqc/templates/benchmarking.py @@ -0,0 +1,46 @@ +#!/usr/bin/env python3 + +import pandas as pd +import json +import platform + +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. + + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str + +df = pd.read_csv("$jaccard", sep='\\t', index_col=0) + +data = { + "id": "benchmarking", + "section_name": "Benchmarking", + "description": "Benchmarking of the tools", + "plot_type": "bargraph", + "data": df.to_dict() +} + +with open("benchmarking_mqc.json", "w") as f: + json.dump(data, f) + +versions = { + "${task.process}" : { + "python": platform.python_version(), + "pandas": pd.__version__ + } +} +with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) \ No newline at end of file diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index 95597227..79cc22d3 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -1,6 +1,7 @@ -include { GNU_SORT as SORT } from '../../modules/nf-core/gnu/sort' -include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge' -include { BEDTOOLS_JACCARD } from '../../modules/nf-core/bedtools/jaccard' +include { GNU_SORT as SORT } from '../../modules/nf-core/gnu/sort' +include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge' +include { BEDTOOLS_JACCARD } from '../../modules/nf-core/bedtools/jaccard' +include { BENCHMARKING_MULTIQC } from '../../modules/local/benchmarking/multiqc' workflow BENCHMARKING { @@ -36,11 +37,15 @@ workflow BENCHMARKING { seed: "tool\tintersection\tunion\tjaccard\tn_intersections") { row -> ["jaccard.tsv", row.join("\t")] } + + BENCHMARKING_MULTIQC(ch_stats) ch_versions = ch_versions.mix(SORT.out.versions) ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) ch_versions = ch_versions.mix(BEDTOOLS_JACCARD.out.versions) + ch_versions = ch_versions.mix(BENCHMARKING_MULTIQC.out.versions) emit: - versions = ch_versions // channel: [ versions.yml ] + reports = BENCHMARKING_MULTIQC.out.report + versions = ch_versions // channel: [ versions.yml ] } diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 23df0513..13a4410a 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -188,6 +188,8 @@ workflow CIRCRNA { CIRCRNA_DISCOVERY_BENCHMARKING.out.tool_bed ) + ch_multiqc_files = ch_multiqc_files.mix(BENCHMARKING.out.reports) + ch_versions = ch_versions.mix(CIRCRNA_DISCOVERY_BENCHMARKING.out.versions) } From d506c8b587ecb753d680c3c4ab37e4b757a91fd2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 25 Apr 2024 19:47:55 +0200 Subject: [PATCH 05/32] Group benchmark multiqc sections --- modules/local/benchmarking/multiqc/main.nf | 4 ++-- .../multiqc/templates/benchmarking.py | 22 +++++++++++-------- 2 files changed, 15 insertions(+), 11 deletions(-) diff --git a/modules/local/benchmarking/multiqc/main.nf b/modules/local/benchmarking/multiqc/main.nf index 5e991ff1..4a366383 100644 --- a/modules/local/benchmarking/multiqc/main.nf +++ b/modules/local/benchmarking/multiqc/main.nf @@ -10,8 +10,8 @@ process BENCHMARKING_MULTIQC { path(jaccard) output: - path("benchmarking_mqc.json"), emit: report - path("versions.yml") , emit: versions + path("*_mqc.json") , emit: report + path("versions.yml"), emit: versions script: template "benchmarking.py" diff --git a/modules/local/benchmarking/multiqc/templates/benchmarking.py b/modules/local/benchmarking/multiqc/templates/benchmarking.py index 86386873..fa1fe401 100644 --- a/modules/local/benchmarking/multiqc/templates/benchmarking.py +++ b/modules/local/benchmarking/multiqc/templates/benchmarking.py @@ -25,16 +25,20 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: df = pd.read_csv("$jaccard", sep='\\t', index_col=0) -data = { - "id": "benchmarking", - "section_name": "Benchmarking", - "description": "Benchmarking of the tools", - "plot_type": "bargraph", - "data": df.to_dict() -} +for metric in df.columns: + data = { + "id": f"benchmarking_{metric}", + "parent_id": "benchmarking", + "parent_name": "Benchmarking", + "parent_description": "Benchmarking of the tools", + "section_name": metric.capitalize(), + "description": f"{metric.capitalize()} values of the tools", + "plot_type": "bargraph", + "data": df[[metric]].T.to_dict() + } -with open("benchmarking_mqc.json", "w") as f: - json.dump(data, f) + with open(f"benchmarking_{metric}_mqc.json", "w") as f: + json.dump(data, f, indent=4) versions = { "${task.process}" : { From fac07a42f6251bd92e8917d6f4441f5cc348f3a2 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Sat, 11 May 2024 10:31:56 +0200 Subject: [PATCH 06/32] implemented location mapping --- .../benchmarking/location_plotting/main.nf | 14 ++++ .../location_plotting/templates/plot_bed.py | 68 +++++++++++++++++++ subworkflows/local/benchmarking.nf | 16 +++-- 3 files changed, 92 insertions(+), 6 deletions(-) create mode 100644 modules/local/benchmarking/location_plotting/main.nf create mode 100644 modules/local/benchmarking/location_plotting/templates/plot_bed.py diff --git a/modules/local/benchmarking/location_plotting/main.nf b/modules/local/benchmarking/location_plotting/main.nf new file mode 100644 index 00000000..5f251d60 --- /dev/null +++ b/modules/local/benchmarking/location_plotting/main.nf @@ -0,0 +1,14 @@ +process PLOT_LOCI { + tag "Plotting loci from ${bed.baseName}" + + input: + tuple val(meta), path(bed) + + output: + path "*.png", emit: plots + + script: + """ + python plot_bed.py ${bed} ${bed.baseName}.png + """ +} diff --git a/modules/local/benchmarking/location_plotting/templates/plot_bed.py b/modules/local/benchmarking/location_plotting/templates/plot_bed.py new file mode 100644 index 00000000..4d59d08d --- /dev/null +++ b/modules/local/benchmarking/location_plotting/templates/plot_bed.py @@ -0,0 +1,68 @@ +#!/usr/bin/env python3 +import sys +import matplotlib.pyplot as plt +from matplotlib.collections import BrokenBarHCollection +import pandas as pd +import platform + +def read_bed(bed_file: str, label: str): + """Read BED file and return as DataFrame with an additional label column for color coding.""" + df = pd.read_csv(bed_file, sep='\t', header=None, names=['chr', 'start', 'end', 'name', 'score', 'strand']) + df['label'] = label + return df + +def plot_bed(datasets: list, output_file: str): + """Plot BED intervals on a genomic track with color coding. + + Args: + datasets (list of tuples): List containing tuples of (DataFrame, color). + output_file (str): Path to save the plot image. + """ + fig, ax = plt.subplots(figsize=(10, 1)) + colors = {'real': 'blue', 'benchmarking': 'red'} + + for data, label in datasets: + chromosome = data['chr'].unique()[0] + intervals = [(row['start'], row['end'] - row['start']) for index, row in data.iterrows()] + yrange = (0, 10) + color = colors[label] + ax.add_collection(BrokenBarHCollection(intervals, yrange, facecolors=color, label=label)) + + ax.set_yticks([]) + ax.set_xlim(min(data['start'].min() for data, label in datasets), max(data['end'].max() for data, label in datasets)) + ax.set_title("Genomic loci by source") + ax.legend(title="Source") + plt.savefig(output_file) + +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string.""" + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\n" + return yaml_str + +def save_versions(): + """Save Python and pandas versions in YAML-like format.""" + versions = { + "plot_bed.py": { + "python": platform.python_version(), + "pandas": pd.__version__ + } + } + with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) + +real_bed_file = sys.argv[1] +benchmarking_bed_file = sys.argv[2] +output_file = sys.argv[3] + +real_data = read_bed(real_bed_file, 'real') +benchmarking_data = read_bed(benchmarking_bed_file, 'benchmarking') + +datasets = [(real_data, 'real'), (benchmarking_data, 'benchmarking')] +plot_bed(datasets, output_file) +save_versions() diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index 79cc22d3..ceee145d 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -2,6 +2,8 @@ include { GNU_SORT as SORT } from '../../modules/nf-core/gnu/sort' include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge' include { BEDTOOLS_JACCARD } from '../../modules/nf-core/bedtools/jaccard' include { BENCHMARKING_MULTIQC } from '../../modules/local/benchmarking/multiqc' +include { PLOT_LOCI } from '../../modules/local/plot_loci' + workflow BENCHMARKING { @@ -18,13 +20,15 @@ workflow BENCHMARKING { tool: meta.tool, benchmarking: meta.benchmarking], bed]} .groupTuple() - + SORT(ch_all) - BEDTOOLS_MERGE(SORT.out.sorted).bed.branch{ meta, bed -> + BEDTOOLS_MERGE(SORT.out.sorted).bed.branch{ meta, bed -> real: !meta.benchmarking benchmarking: meta.benchmarking }.set { ch_merged } + PLOT_LOCI(ch_merged.real) + ch_joined = ch_merged.real.map{ meta, bed -> [[id: meta.tool], bed]} .join(ch_merged.benchmarking.map{ meta, bed -> [[id: meta.tool], bed]}) @@ -32,12 +36,12 @@ workflow BENCHMARKING { ch_stats = ch_jaccard.splitCsv(header: true, sep: "\t") .map{ meta, values -> [meta.id, values.intersection, values.union, values.jaccard, values.n_intersections]} - .collectFile( newLine: true, - storeDir: params.outdir, - seed: "tool\tintersection\tunion\tjaccard\tn_intersections") { + .collectFile( newLine: true, + storeDir: params.outdir, + seed: "tool\tintersection\tunion\tjaccard\tn_intersections") { row -> ["jaccard.tsv", row.join("\t")] } - + BENCHMARKING_MULTIQC(ch_stats) ch_versions = ch_versions.mix(SORT.out.versions) From a1a9594b2e4fd4877679387c0f7975c92bb0d646 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fabian=20B=C3=B6hm?= Date: Mon, 13 May 2024 13:20:14 +0200 Subject: [PATCH 07/32] diagnostics: ch_joined not found, added files --- modules/local/benchmarking/bed_to_csv/main.nf | 22 +++++++++++++++++++ .../bed_to_csv/templates/starts_bed.py | 16 ++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 modules/local/benchmarking/bed_to_csv/main.nf create mode 100644 modules/local/benchmarking/bed_to_csv/templates/starts_bed.py diff --git a/modules/local/benchmarking/bed_to_csv/main.nf b/modules/local/benchmarking/bed_to_csv/main.nf new file mode 100644 index 00000000..e33e889b --- /dev/null +++ b/modules/local/benchmarking/bed_to_csv/main.nf @@ -0,0 +1,22 @@ +process BED_TO_CSV { + label "process_single" + + conda "bioconda::pandas=1.5.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'biocontainers/pandas:1.5.2' }" + + input: + tuple val(id), path(bedfile1), path(bedfile2) from ch_joined + output: + path "${bedfile1.baseName}.csv" + path "${bedfile2.baseName}.csv" + script: + + """ + echo 'Process start' + """ + template "process_bedfiles.py $bedfile1 ${bedfile1.baseName}.csv $bedfile2 ${bedfile2.baseName}.csv" + + +} \ No newline at end of file diff --git a/modules/local/benchmarking/bed_to_csv/templates/starts_bed.py b/modules/local/benchmarking/bed_to_csv/templates/starts_bed.py new file mode 100644 index 00000000..ef988400 --- /dev/null +++ b/modules/local/benchmarking/bed_to_csv/templates/starts_bed.py @@ -0,0 +1,16 @@ +import pandas as pd +import sys + +# Command line arguments +input_bed_file_1 = sys.argv[1] +output_csv_file_1 = sys.argv[2] +input_bed_file_2 = sys.argv[3] +output_csv_file_2 = sys.argv[4] + +# Process the first BED file +data1 = pd.read_csv(input_bed_file_1, sep='\t', header=None, usecols=[0, 1, 5], names=['chromosome', 'start', 'strand']) +data1.to_csv(output_csv_file_1, index=False) + +# Process the second BED file +data2 = pd.read_csv(input_bed_file_2, sep='\t', header=None, usecols=[0, 1, 5], names=['chromosome', 'start', 'strand']) +data2.to_csv(output_csv_file_2, index=False) \ No newline at end of file From 9c1aae16064753d403374237ad6d60c2eab725e4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fabian=20B=C3=B6hm?= Date: Wed, 5 Jun 2024 10:21:06 +0200 Subject: [PATCH 08/32] Added Overlap location plots --- .../local/benchmarking/location_plots/main.nf | 13 ++ .../location_plots/templates/create_plots.py | 118 ++++++++++++++++++ .../local/benchmarking/overlap_plot/main.nf | 14 +++ .../overlap_plot/templates/create_plots.py | 42 +++++++ 4 files changed, 187 insertions(+) create mode 100644 modules/local/benchmarking/location_plots/main.nf create mode 100755 modules/local/benchmarking/location_plots/templates/create_plots.py create mode 100644 modules/local/benchmarking/overlap_plot/main.nf create mode 100644 modules/local/benchmarking/overlap_plot/templates/create_plots.py diff --git a/modules/local/benchmarking/location_plots/main.nf b/modules/local/benchmarking/location_plots/main.nf new file mode 100644 index 00000000..fa3e3932 --- /dev/null +++ b/modules/local/benchmarking/location_plots/main.nf @@ -0,0 +1,13 @@ +process LOCATION_PLOT { + label "process_single" + + conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2" + container 'uphl/seaborn' + + input: + tuple val(id), path(bedfile1), path(bedfile2) + output: + path("*_mqc.png") , emit: report + script: + template "create_plots.py" +} \ No newline at end of file diff --git a/modules/local/benchmarking/location_plots/templates/create_plots.py b/modules/local/benchmarking/location_plots/templates/create_plots.py new file mode 100755 index 00000000..265e4605 --- /dev/null +++ b/modules/local/benchmarking/location_plots/templates/create_plots.py @@ -0,0 +1,118 @@ +#!/usr/bin/env python3 +import csv +import os +import matplotlib.pyplot as plt +import seaborn as sns +import pandas as pd +from matplotlib.lines import Line2D + +# Inputs directly from Nextflow variables +input_bed_file_1 = '$bedfile1' +input_bed_file_2 = '$bedfile2' + +# Read input files function +def read_bed_file(file_path, label): + data = {'chromosome': [], 'start': [], 'strand': [], 'file_label': []} + with open(file_path, 'r') as file: + reader = csv.reader(file, delimiter='\t') + for row in reader: + data['chromosome'].append(row[0]) + data['start'].append(int(row[1])) + data['strand'].append(row[3]) # Assuming strand information is in the 4th column + data['file_label'].append(label) # Label to indicate the source file + return data + +# Combine data function +def combine_data(data1, data2): + for key in data1: + data1[key].extend(data2[key]) + return data1 + +data1 = read_bed_file(input_bed_file_1, 'real') +data2 = read_bed_file(input_bed_file_2, 'benchmark') + +# Combine the two datasets +combined_data = combine_data(data1, data2) + +# Create a DataFrame +df = pd.DataFrame({ + 'Chromosome': combined_data['chromosome'], + 'Start Location': combined_data['start'], + 'Strand': combined_data['strand'], + 'File Label': combined_data['file_label'] +}) + +# Combine File Label and Strand into a single column for easier plotting +df['File_Strand'] = df['File Label'] + ' ' + df['Strand'] + +# Separate the data by strand +df_plus = df[df['Strand'] == '+'] +df_minus = df[df['Strand'] == '-'] + +# Create figure and axes +fig, ax = plt.subplots(figsize=(12, 6)) + +# Define the color palette +palette_plus = { + "real +": "red", + "benchmark +": "blue" +} +palette_minus = { + "real -": "lightcoral", + "benchmark -": "lightblue" +} + +# Draw violins for the + strand +sns.violinplot( + x="Chromosome", + y="Start Location", + hue="File_Strand", + data=df_plus, + palette=palette_plus, + split=True, + ax=ax, + scale="count", + scale_hue=False, + saturation=0.75, + inner=None +) + +# Draw violins for the - strand +sns.violinplot( + x="Chromosome", + y="Start Location", + hue="File_Strand", + data=df_minus, + palette=palette_minus, + split=True, + ax=ax, + scale="count", + scale_hue=False, + saturation=0.75, + inner=None +) + +# Set transparency for all violins +for violin in ax.collections: + violin.set_alpha(0.25) + +# Compose a custom legend +custom_lines = [ + Line2D([0], [0], color=color, lw=4, alpha=0.25) + for color in palette_plus.values() +] + [ + Line2D([0], [0], color=color, lw=4, alpha=0.25) + for color in palette_minus.values() +] +ax.legend( + custom_lines, + list(palette_plus.keys()) + list(palette_minus.keys()), + title="File : Strand" +) + +plt.title('Start Locations of circRNA by Chromosome and Strand') +plot_file_name = f"{input_bed_file_1.replace('.bed','')}_{input_bed_file_2.replace('.bed','')}_mqc.png" +# Save the plot +plt.savefig(plot_file_name, bbox_inches='tight') + + diff --git a/modules/local/benchmarking/overlap_plot/main.nf b/modules/local/benchmarking/overlap_plot/main.nf new file mode 100644 index 00000000..0315b575 --- /dev/null +++ b/modules/local/benchmarking/overlap_plot/main.nf @@ -0,0 +1,14 @@ +process OVERLAP_PLOT { + label "process_single" + + conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2" + container 'uphl/seaborn' + + input: + tuple val(meta), path(bed) + path "versions.yml" + output: + path("*_mqc.png") , emit: report + script: + template "create_plots.py" +} \ No newline at end of file diff --git a/modules/local/benchmarking/overlap_plot/templates/create_plots.py b/modules/local/benchmarking/overlap_plot/templates/create_plots.py new file mode 100644 index 00000000..892a788b --- /dev/null +++ b/modules/local/benchmarking/overlap_plot/templates/create_plots.py @@ -0,0 +1,42 @@ +#!/usr/bin/env python3 +import csv +import os +import matplotlib.pyplot as plt +import seaborn as sns +import pandas as pd + +# Input directly from Nextflow variable +input_bed_file = '$bed' + +# Read input file function +def read_bed_file(file_path): + data = {'chromosome': [], 'start': [], 'strand': []} + with open(file_path, 'r') as file: + reader = csv.reader(file, delimiter='\t') + for row in reader: + data['chromosome'].append(row[0]) + data['start'].append(int(row[1])) + data['strand'].append(row[3]) + return data + +# Read the data +data = read_bed_file(input_bed_file) + +# Create a DataFrame for seaborn +df = pd.DataFrame({ + 'Chromosome': data['chromosome'], + 'Start Location': data['start'], + 'Strand': data['strand'] +}) + +# Plotting +plt.figure(figsize=(12, 6)) +sns.violinplot(x='Chromosome', y='Start Location', hue='Strand', data=df, split=True, inner="quartile") +plt.title('Start Locations of circRNA by Chromosome and Strand') +plt.legend(title="Strand") +plot_file_name = f"{input_bed_file.replace('.bed','')}_overlaps_mqc.png" + +# Save the plot +plt.savefig(plot_file_name, bbox_inches='tight') +print("Plot saved as:", plot_file_name) +print("Current working directory:", os.getcwd()) From 31ff400a647613ac026db412e256028b53988f0e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fabian=20B=C3=B6hm?= Date: Thu, 6 Jun 2024 23:39:30 +0200 Subject: [PATCH 09/32] prepare seq_depth data, trimgalore reports in benchmarking.nf --- .../local/benchmarking/seq_depth_plot/main.nf | 14 ++ .../seq_depth_plot/templates/create_plots.py | 13 ++ modules/local/benchmarking/write_file/main.nf | 13 ++ .../write_file/templates/write.py | 11 ++ .../bedtools/genomecov/environment.yml | 7 + modules/nf-core/bedtools/genomecov/main.nf | 74 +++++++++++ modules/nf-core/bedtools/genomecov/meta.yml | 59 +++++++++ .../bedtools/genomecov/tests/main.nf.test | 122 ++++++++++++++++++ .../genomecov/tests/main.nf.test.snap | 95 ++++++++++++++ .../bedtools/genomecov/tests/nextflow.config | 7 + .../nf-core/bedtools/genomecov/tests/tags.yml | 2 + 11 files changed, 417 insertions(+) create mode 100644 modules/local/benchmarking/seq_depth_plot/main.nf create mode 100644 modules/local/benchmarking/seq_depth_plot/templates/create_plots.py create mode 100644 modules/local/benchmarking/write_file/main.nf create mode 100644 modules/local/benchmarking/write_file/templates/write.py create mode 100644 modules/nf-core/bedtools/genomecov/environment.yml create mode 100644 modules/nf-core/bedtools/genomecov/main.nf create mode 100644 modules/nf-core/bedtools/genomecov/meta.yml create mode 100644 modules/nf-core/bedtools/genomecov/tests/main.nf.test create mode 100644 modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap create mode 100644 modules/nf-core/bedtools/genomecov/tests/nextflow.config create mode 100644 modules/nf-core/bedtools/genomecov/tests/tags.yml diff --git a/modules/local/benchmarking/seq_depth_plot/main.nf b/modules/local/benchmarking/seq_depth_plot/main.nf new file mode 100644 index 00000000..2e294562 --- /dev/null +++ b/modules/local/benchmarking/seq_depth_plot/main.nf @@ -0,0 +1,14 @@ +process SEQ_DEPTH_CORRELLATION { + label "process_single" + + conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2" + container 'uphl/seaborn' + + input: + path(depth) + tuple val(meta), path(bed) + output: + path("*.txt") , optional:true, emit: report + script: + template "create_plots.py" +} \ No newline at end of file diff --git a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py new file mode 100644 index 00000000..ed769839 --- /dev/null +++ b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py @@ -0,0 +1,13 @@ +#!/usr/bin/env python3 +import os +meta1 = "$meta" +depth = "$depth" +bed = "$bed" + +with open("output.txt", "w") as file: + # Write the variables to the file + depth = os.path.abspath(depth) + bed = os.path.abspath(bed) + file.write(meta1) + file.write(depth) + file.write(bed) \ No newline at end of file diff --git a/modules/local/benchmarking/write_file/main.nf b/modules/local/benchmarking/write_file/main.nf new file mode 100644 index 00000000..317ae47a --- /dev/null +++ b/modules/local/benchmarking/write_file/main.nf @@ -0,0 +1,13 @@ +process WRITE { + label "process_single" + + conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2" + container 'uphl/seaborn' + + input: + tuple val(meta), path(value) + output: + path("*.txt") , optional:true, emit: report + script: + template "write.py" +} \ No newline at end of file diff --git a/modules/local/benchmarking/write_file/templates/write.py b/modules/local/benchmarking/write_file/templates/write.py new file mode 100644 index 00000000..7772556d --- /dev/null +++ b/modules/local/benchmarking/write_file/templates/write.py @@ -0,0 +1,11 @@ +#!/usr/bin/env python3 +import os +m = "$meta" +v = "$value" + + +with open("output.txt", "w") as file: + # Write the variables to the file + v = os.path.abspath(v) + file.write(m + '\t') + file.write(v) \ No newline at end of file diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml new file mode 100644 index 00000000..8fbe20c3 --- /dev/null +++ b/modules/nf-core/bedtools/genomecov/environment.yml @@ -0,0 +1,7 @@ +name: bedtools_genomecov +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf new file mode 100644 index 00000000..954e8913 --- /dev/null +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -0,0 +1,74 @@ +process BEDTOOLS_GENOMECOV { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" + + input: + tuple val(meta), path(intervals), val(scale) + path sizes + val extension + val sort + + output: + tuple val(meta), path("*.${extension}"), emit: genomecov + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args_list = args.tokenize() + args += (scale > 0 && scale != 1) ? " -scale $scale" : "" + if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) { + args += " -bg" + } + def sort_cmd = sort ? '| bedtools sort' : '' + + def prefix = task.ext.prefix ?: "${meta.id}" + if (intervals.name =~ /\.bam/) { + """ + bedtools \\ + genomecov \\ + -ibam $intervals \\ + $args \\ + $sort_cmd \\ + > ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ + } else { + """ + bedtools \\ + genomecov \\ + -i $intervals \\ + -g $sizes \\ + $args \\ + $sort_cmd \\ + > ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ + } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/bedtools/genomecov/meta.yml b/modules/nf-core/bedtools/genomecov/meta.yml new file mode 100644 index 00000000..2b2385e3 --- /dev/null +++ b/modules/nf-core/bedtools/genomecov/meta.yml @@ -0,0 +1,59 @@ +name: bedtools_genomecov +description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. +keywords: + - bed + - bam + - genomecov + - bedtools + - histogram +tools: + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bam|bed|gff|vcf}" + - scale: + type: integer + description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch + - sizes: + type: file + description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column + - extension: + type: string + description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genomecov: + type: file + description: Computed genome coverage file + pattern: "*.${extension}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@edmundmiller" + - "@sruthipsuresh" + - "@drpatelh" + - "@sidorov-si" + - "@chris-cheshire" +maintainers: + - "@edmundmiller" + - "@sruthipsuresh" + - "@drpatelh" + - "@sidorov-si" + - "@chris-cheshire" diff --git a/modules/nf-core/bedtools/genomecov/tests/main.nf.test b/modules/nf-core/bedtools/genomecov/tests/main.nf.test new file mode 100644 index 00000000..8213cff9 --- /dev/null +++ b/modules/nf-core/bedtools/genomecov/tests/main.nf.test @@ -0,0 +1,122 @@ +nextflow_process { + name "Test Process BEDTOOLS_GENOMECOV" + script "../main.nf" + process "BEDTOOLS_GENOMECOV" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/genomecov" + + test("sarscov2 - no scale") { + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true), + 1 + ] + // sizes + input[1] = [] + // extension + input[2] = "txt" + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("no_scale") } + ) + } + + } + + test("sarscov2 - dummy sizes") { + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true), + 0.5 + ] + // sizes + input[1] = file('dummy_chromosome_sizes') + // extension + input[2] = 'txt' + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("dummy_sizes") } + ) + } + + } + + test("sarscov2 - scale") { + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/baits.bed", checkIfExists: true), + 0.5 + ] + // sizes + input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.sizes", checkIfExists: true) + // extension + input[2] = 'txt' + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("scale") } + ) + } + + } + + test("stub") { + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true), + 1 + ] + // sizes + input[1] = [] + // extension + input[2] = 'txt' + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.genomecov[0][1]).name).match("stub") } + ) + } + + } + +} diff --git a/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap b/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap new file mode 100644 index 00000000..8f9191e4 --- /dev/null +++ b/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap @@ -0,0 +1,95 @@ +{ + "dummy_sizes": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.coverage.txt:md5,01291b6e1beab72e046653e709eb0e10" + ] + ], + "1": [ + "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + ], + "genomecov": [ + [ + { + "id": "test" + }, + "test.coverage.txt:md5,01291b6e1beab72e046653e709eb0e10" + ] + ], + "versions": [ + "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + ] + } + ], + "timestamp": "2023-12-05T17:35:58.35232" + }, + "no_scale": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.coverage.txt:md5,66083198daca6c001d328ba9616e9b53" + ] + ], + "1": [ + "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + ], + "genomecov": [ + [ + { + "id": "test" + }, + "test.coverage.txt:md5,66083198daca6c001d328ba9616e9b53" + ] + ], + "versions": [ + "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + ] + } + ], + "timestamp": "2023-12-05T17:35:51.142496" + }, + "stub": { + "content": [ + "test.coverage.txt" + ], + "timestamp": "2023-12-05T17:36:13.084709" + }, + "scale": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.coverage.txt:md5,de3c59c0ea123bcdbbad27bc0a0a601e" + ] + ], + "1": [ + "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + ], + "genomecov": [ + [ + { + "id": "test" + }, + "test.coverage.txt:md5,de3c59c0ea123bcdbbad27bc0a0a601e" + ] + ], + "versions": [ + "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + ] + } + ], + "timestamp": "2023-12-05T17:36:05.962006" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/genomecov/tests/nextflow.config b/modules/nf-core/bedtools/genomecov/tests/nextflow.config new file mode 100644 index 00000000..bdb74ae5 --- /dev/null +++ b/modules/nf-core/bedtools/genomecov/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: BEDTOOLS_GENOMECOV { + ext.prefix = { "${meta.id}.coverage" } + } + +} diff --git a/modules/nf-core/bedtools/genomecov/tests/tags.yml b/modules/nf-core/bedtools/genomecov/tests/tags.yml new file mode 100644 index 00000000..55fce478 --- /dev/null +++ b/modules/nf-core/bedtools/genomecov/tests/tags.yml @@ -0,0 +1,2 @@ +bedtools/genomecov: + - "modules/nf-core/bedtools/genomecov/**" From 1d036fb8d0d56637bfafb2a8f54cbdfb1d264847 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fabian=20B=C3=B6hm?= Date: Tue, 18 Jun 2024 11:14:31 +0200 Subject: [PATCH 10/32] sequencing depth pearson correllation computation --- .../local/benchmarking/seq_depth_plot/main.nf | 7 +- .../seq_depth_plot/templates/create_plots.py | 75 ++++++++++++++++--- subworkflows/local/benchmarking.nf | 67 +++++++++++++++-- subworkflows/local/circrna_discovery.nf | 1 + workflows/circrna/main.nf | 5 +- 5 files changed, 133 insertions(+), 22 deletions(-) diff --git a/modules/local/benchmarking/seq_depth_plot/main.nf b/modules/local/benchmarking/seq_depth_plot/main.nf index 2e294562..17e130b9 100644 --- a/modules/local/benchmarking/seq_depth_plot/main.nf +++ b/modules/local/benchmarking/seq_depth_plot/main.nf @@ -2,13 +2,12 @@ process SEQ_DEPTH_CORRELLATION { label "process_single" conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2" - container 'uphl/seaborn' + container 'https://depot.galaxyproject.org/singularity/bionumpy:0.2.12--pyha8f3691_0' input: - path(depth) - tuple val(meta), path(bed) + tuple val(meta), path(bed), path(depth) output: - path("*.txt") , optional:true, emit: report + path("*.txt") , emit: report script: template "create_plots.py" } \ No newline at end of file diff --git a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py index ed769839..d868c739 100644 --- a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py +++ b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py @@ -1,13 +1,70 @@ #!/usr/bin/env python3 -import os -meta1 = "$meta" +import logging +import numpy as np + +# Initialize logging +logging.basicConfig(filename='process_log.log', level=logging.DEBUG, format='%(asctime)s - %(levelname)s - %(message)s') + +meta = "$meta" depth = "$depth" bed = "$bed" -with open("output.txt", "w") as file: - # Write the variables to the file - depth = os.path.abspath(depth) - bed = os.path.abspath(bed) - file.write(meta1) - file.write(depth) - file.write(bed) \ No newline at end of file +def extract_matching_paths(array, filepath): + array_id = array.split(",")[0].split(":")[1] + matching_paths = [] + with open(filepath, 'r') as file: + for line in file: + line_id = line.split(",")[0].split(":")[1] + if array_id == line_id: + path = line.split()[-1] + matching_paths.append(path) + return matching_paths + +def calculate_correlation(bed_file_path, depth_file_path): + # Read the BED file and store circRNA regions + circRNA_regions = [] + with open(bed_file_path, 'r') as bed_file: + for line in bed_file: + parts = line.strip().split() + chr = parts[0] + start = int(parts[1]) + end = int(parts[2]) + circRNA_regions.append((chr, start, end)) + + # Read the sequence depth file + circRNA_presence = [] + sequencing_depth = [] + + with open(depth_file_path, 'r') as depth_file: + bed_idx = 0 + bed_len = len(circRNA_regions) + + for line in depth_file: + parts = line.strip().split() + chr = parts[0] + pos = int(parts[1]) + depth = int(parts[2]) + + # Move bed_idx to the correct region + while bed_idx < bed_len and (circRNA_regions[bed_idx][0] < chr or (circRNA_regions[bed_idx][0] == chr and circRNA_regions[bed_idx][2] < pos)): + bed_idx += 1 + + # Check if the current position is within a circRNA region + if bed_idx < bed_len and circRNA_regions[bed_idx][0] == chr and circRNA_regions[bed_idx][1] <= pos <= circRNA_regions[bed_idx][2]: + circRNA_presence.append(1) + else: + circRNA_presence.append(0) + + sequencing_depth.append(depth) + + # Calculate the correlation coefficient + correlation = np.corrcoef(sequencing_depth, circRNA_presence)[0, 1] + + return correlation + +with open('stats.txt', 'w') as outfile: + for path in extract_matching_paths(meta, depth): + corr = calculate_correlation(bed, path) + output_line = meta.split(",")[3] + ' ' + str(corr) + outfile.write(output_line) + logging.debug(f'Written to stats.txt: {output_line.strip()}') diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index ceee145d..f6a3e748 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -1,8 +1,14 @@ -include { GNU_SORT as SORT } from '../../modules/nf-core/gnu/sort' -include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge' -include { BEDTOOLS_JACCARD } from '../../modules/nf-core/bedtools/jaccard' -include { BENCHMARKING_MULTIQC } from '../../modules/local/benchmarking/multiqc' -include { PLOT_LOCI } from '../../modules/local/plot_loci' +include { GNU_SORT as SORT } from '../../modules/nf-core/gnu/sort' +include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge' +include { BEDTOOLS_INTERSECT } from '../../modules/nf-core/bedtools/intersect' +include { BEDTOOLS_JACCARD } from '../../modules/nf-core/bedtools/jaccard' +include { BEDTOOLS_GENOMECOV } from '../../modules/nf-core/bedtools/genomecov' +include { BENCHMARKING_MULTIQC } from '../../modules/local/benchmarking/multiqc' +include { LOCATION_PLOT } from '../../modules/local/benchmarking/location_plots' +include { OVERLAP_PLOT } from '../../modules/local/benchmarking/overlap_plot' +include { SEQ_DEPTH_CORRELLATION} from '../../modules/local/benchmarking/seq_depth_plot' +include { WRITE } from '../../modules/local/benchmarking/write_file' +include { WRITE as WRITE2 } from '../../modules/local/benchmarking/write_file' workflow BENCHMARKING { @@ -10,6 +16,9 @@ workflow BENCHMARKING { take: ch_real_bed ch_benchmarking_bed + ch_real_bam + ch_benchmarking_bam + ch_trim_report main: @@ -22,16 +31,55 @@ workflow BENCHMARKING { .groupTuple() SORT(ch_all) + BEDTOOLS_MERGE(SORT.out.sorted).bed.branch{ meta, bed -> real: !meta.benchmarking benchmarking: meta.benchmarking }.set { ch_merged } - PLOT_LOCI(ch_merged.real) + ch_merged.real.view {"emits: $it"} ch_joined = ch_merged.real.map{ meta, bed -> [[id: meta.tool], bed]} .join(ch_merged.benchmarking.map{ meta, bed -> [[id: meta.tool], bed]}) + ch_intersect = BEDTOOLS_INTERSECT(ch_joined,[[], []]) + + OVERLAP_PLOT(ch_intersect) + + LOCATION_PLOT(ch_joined) + + ch_meta = ch_real_bam.map { it[0] } + ch_path = ch_real_bam.map { it[1] } + ch_scale = Channel.value(1) + ch_genomecov_inputs = ch_meta.combine(ch_path).combine(ch_scale) + .map { meta, path, scale -> + tuple(meta, path, scale) + } + + ch_genomecov = BEDTOOLS_GENOMECOV(ch_genomecov_inputs, [], "bg",false) + + ch_depthfile = WRITE(ch_genomecov.genomecov).flatten() + .collectFile(storeDir: params.outdir, newLine: true) { file -> + def content = file.text + return ['genomecovs.txt', content] + } + + ch_meta = ch_joined.map { it[0] } + ch_path = ch_joined.map { it[1] } + ch_corr_inputs = ch_meta.combine(ch_path) + + ch_real_bed.combine(ch_depthfile) + .flatMap { bed, depthfile -> + def (meta, bed_path) = bed + [meta, bed_path, depthfile] + } + .set { ch_depth_correlation } + + ch_depth_correlation.collect() + .collectFile(name: 'corr.txt', storeDir: params.outdir, newLine: true) { file -> + file.collect { it.text }.join('\n') + } + ch_jaccard = BEDTOOLS_JACCARD(ch_joined, [[], []]).tsv ch_stats = ch_jaccard.splitCsv(header: true, sep: "\t") @@ -49,7 +97,10 @@ workflow BENCHMARKING { ch_versions = ch_versions.mix(BEDTOOLS_JACCARD.out.versions) ch_versions = ch_versions.mix(BENCHMARKING_MULTIQC.out.versions) + ch_reports = BENCHMARKING_MULTIQC.out.report.mix(LOCATION_PLOT.out.report) + ch_reports = ch_reports.mix(OVERLAP_PLOT.out.report) + emit: - reports = BENCHMARKING_MULTIQC.out.report + reports = ch_reports versions = ch_versions // channel: [ versions.yml ] -} +} \ No newline at end of file diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index c4218ca0..39889edc 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -161,6 +161,7 @@ workflow CIRCRNA_DISCOVERY { annotation_gtf = ANNOTATION.out.gtf counts_bed = MERGE_SAMPLES.out.counts_bed counts_tsv = MERGE_SAMPLES.out.counts_tsv + star_bam = STAR_2ND_PASS.out.bam multiqc_files = ch_multiqc_files versions = ch_versions diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 13a4410a..88c4e16c 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -185,7 +185,10 @@ workflow CIRCRNA { BENCHMARKING( CIRCRNA_DISCOVERY.out.tool_bed, - CIRCRNA_DISCOVERY_BENCHMARKING.out.tool_bed + CIRCRNA_DISCOVERY_BENCHMARKING.out.tool_bed, + CIRCRNA_DISCOVERY.out.star_bam, + CIRCRNA_DISCOVERY_BENCHMARKING.out.star_bam, + FASTQC_TRIMGALORE.out.trim_log ) ch_multiqc_files = ch_multiqc_files.mix(BENCHMARKING.out.reports) From bda9c5927f80ba0466495d30308e6754725f4f8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fabian=20B=C3=B6hm?= Date: Tue, 18 Jun 2024 11:19:39 +0200 Subject: [PATCH 11/32] config files added to git --- conf/modules.config | 8 ++++ modules.json | 105 +++++++++++++++++++++++++++++++++----------- 2 files changed, 88 insertions(+), 25 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 20c77055..78ce6d52 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -630,6 +630,14 @@ process { ext.suffix = "combined.bed" } + withName: '.*:BENCHMARKING:BEDTOOLS_MERGE' { + ext.args = "-s -c 6 -o distinct" + } + + withName: '.*:BENCHMARKING:BEDTOOLS_GENOMECOV' { + ext.args = "-dz" + } + withName: COMBINE_TRANSCRIPTOME_GTFS { ext.args = "-k 1,1 -k4,4n -k5,5n" ext.suffix = "gtf" diff --git a/modules.json b/modules.json index 1b54424a..ca3e3065 100644 --- a/modules.json +++ b/modules.json @@ -5,6 +5,13 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { + "bedtools/genomecov": { + "branch": "master", + "git_sha": "81b90194ce9911dbd55bba2c65c6919f6677abc4", + "installed_by": [ + "modules" + ] + }, "bedtools/getfasta": { "branch": "master", "git_sha": "cdcdd5e3d806f0ff3983c40c69e0b07bb44ec299", @@ -13,32 +20,44 @@ "bedtools/intersect": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/jaccard": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/merge": { "branch": "master", "git_sha": "a5377837fe9013bde89de8689829e83e84086536", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/sort": { "branch": "master", "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bowtie/align": { "branch": "master", "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bowtie/build": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bowtie2/align": { "branch": "master", @@ -48,7 +67,9 @@ "bowtie2/build": { "branch": "master", "git_sha": "1fea64f5132a813ec97c1c6d3a74e0aee7142b6d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/index": { "branch": "master", @@ -58,7 +79,9 @@ "cat/cat": { "branch": "master", "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", @@ -68,12 +91,16 @@ "circexplorer2/annotate": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "circexplorer2/parse": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "csvtk/join": { "branch": "master", @@ -88,12 +115,16 @@ "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/tx2gene": { "branch": "master", "git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastqc": { "branch": "master", @@ -113,27 +144,37 @@ "hisat2/align": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "hisat2/build": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "hisat2/extractsplicesites": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "miranda": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", @@ -178,27 +219,37 @@ "segemehl/index": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "star/align": { "branch": "master", "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "star/genomegenerate": { "branch": "master", "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "stringtie/stringtie": { "branch": "master", "git_sha": "b1b959609bda44341120aed1766329909f54b8d0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "trimgalore": { "branch": "master", "git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tximeta/tximport": { "branch": "master", @@ -222,7 +273,9 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", @@ -232,10 +285,12 @@ "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file From e0bc4f0507c15998b5a250d8a942bff2e1bd6928 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Tue, 18 Jun 2024 15:08:43 +0200 Subject: [PATCH 12/32] Postmerge fixes --- conf/modules.config | 13 +--- modules/local/benchmarking/bed_to_csv/main.nf | 22 ------ .../bed_to_csv/templates/starts_bed.py | 16 ----- .../benchmarking/location_plotting/main.nf | 14 ---- .../location_plotting/templates/plot_bed.py | 68 ------------------- subworkflows/local/benchmarking.nf | 13 ---- subworkflows/local/circrna_discovery.nf | 2 +- subworkflows/local/discovery/star2pass.nf | 1 + workflows/circrna/main.nf | 5 +- 9 files changed, 6 insertions(+), 148 deletions(-) delete mode 100644 modules/local/benchmarking/bed_to_csv/main.nf delete mode 100644 modules/local/benchmarking/bed_to_csv/templates/starts_bed.py delete mode 100644 modules/local/benchmarking/location_plotting/main.nf delete mode 100644 modules/local/benchmarking/location_plotting/templates/plot_bed.py diff --git a/conf/modules.config b/conf/modules.config index 78ce6d52..e6fd3789 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -625,17 +625,8 @@ process { ext.suffix = "unique.bed" } - withName: '.*:BENCHMARKING:SORT' { - ext.args = "-k 1,1 -k2,2n -k3,3n -u" - ext.suffix = "combined.bed" - } - - withName: '.*:BENCHMARKING:BEDTOOLS_MERGE' { - ext.args = "-s -c 6 -o distinct" - } - - withName: '.*:BENCHMARKING:BEDTOOLS_GENOMECOV' { - ext.args = "-dz" + withName: '.*:CIRCRNA_DISCOVERY_BENCHMARKING:ANNOTATION:REMOVE_SCORE_STRAND' { + ext.suffix = "_benchmarking.tidy.bed" } withName: COMBINE_TRANSCRIPTOME_GTFS { diff --git a/modules/local/benchmarking/bed_to_csv/main.nf b/modules/local/benchmarking/bed_to_csv/main.nf deleted file mode 100644 index e33e889b..00000000 --- a/modules/local/benchmarking/bed_to_csv/main.nf +++ /dev/null @@ -1,22 +0,0 @@ -process BED_TO_CSV { - label "process_single" - - conda "bioconda::pandas=1.5.2" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : - 'biocontainers/pandas:1.5.2' }" - - input: - tuple val(id), path(bedfile1), path(bedfile2) from ch_joined - output: - path "${bedfile1.baseName}.csv" - path "${bedfile2.baseName}.csv" - script: - - """ - echo 'Process start' - """ - template "process_bedfiles.py $bedfile1 ${bedfile1.baseName}.csv $bedfile2 ${bedfile2.baseName}.csv" - - -} \ No newline at end of file diff --git a/modules/local/benchmarking/bed_to_csv/templates/starts_bed.py b/modules/local/benchmarking/bed_to_csv/templates/starts_bed.py deleted file mode 100644 index ef988400..00000000 --- a/modules/local/benchmarking/bed_to_csv/templates/starts_bed.py +++ /dev/null @@ -1,16 +0,0 @@ -import pandas as pd -import sys - -# Command line arguments -input_bed_file_1 = sys.argv[1] -output_csv_file_1 = sys.argv[2] -input_bed_file_2 = sys.argv[3] -output_csv_file_2 = sys.argv[4] - -# Process the first BED file -data1 = pd.read_csv(input_bed_file_1, sep='\t', header=None, usecols=[0, 1, 5], names=['chromosome', 'start', 'strand']) -data1.to_csv(output_csv_file_1, index=False) - -# Process the second BED file -data2 = pd.read_csv(input_bed_file_2, sep='\t', header=None, usecols=[0, 1, 5], names=['chromosome', 'start', 'strand']) -data2.to_csv(output_csv_file_2, index=False) \ No newline at end of file diff --git a/modules/local/benchmarking/location_plotting/main.nf b/modules/local/benchmarking/location_plotting/main.nf deleted file mode 100644 index 5f251d60..00000000 --- a/modules/local/benchmarking/location_plotting/main.nf +++ /dev/null @@ -1,14 +0,0 @@ -process PLOT_LOCI { - tag "Plotting loci from ${bed.baseName}" - - input: - tuple val(meta), path(bed) - - output: - path "*.png", emit: plots - - script: - """ - python plot_bed.py ${bed} ${bed.baseName}.png - """ -} diff --git a/modules/local/benchmarking/location_plotting/templates/plot_bed.py b/modules/local/benchmarking/location_plotting/templates/plot_bed.py deleted file mode 100644 index 4d59d08d..00000000 --- a/modules/local/benchmarking/location_plotting/templates/plot_bed.py +++ /dev/null @@ -1,68 +0,0 @@ -#!/usr/bin/env python3 -import sys -import matplotlib.pyplot as plt -from matplotlib.collections import BrokenBarHCollection -import pandas as pd -import platform - -def read_bed(bed_file: str, label: str): - """Read BED file and return as DataFrame with an additional label column for color coding.""" - df = pd.read_csv(bed_file, sep='\t', header=None, names=['chr', 'start', 'end', 'name', 'score', 'strand']) - df['label'] = label - return df - -def plot_bed(datasets: list, output_file: str): - """Plot BED intervals on a genomic track with color coding. - - Args: - datasets (list of tuples): List containing tuples of (DataFrame, color). - output_file (str): Path to save the plot image. - """ - fig, ax = plt.subplots(figsize=(10, 1)) - colors = {'real': 'blue', 'benchmarking': 'red'} - - for data, label in datasets: - chromosome = data['chr'].unique()[0] - intervals = [(row['start'], row['end'] - row['start']) for index, row in data.iterrows()] - yrange = (0, 10) - color = colors[label] - ax.add_collection(BrokenBarHCollection(intervals, yrange, facecolors=color, label=label)) - - ax.set_yticks([]) - ax.set_xlim(min(data['start'].min() for data, label in datasets), max(data['end'].max() for data, label in datasets)) - ax.set_title("Genomic loci by source") - ax.legend(title="Source") - plt.savefig(output_file) - -def format_yaml_like(data: dict, indent: int = 0) -> str: - """Formats a dictionary to a YAML-like string.""" - yaml_str = "" - for key, value in data.items(): - spaces = " " * indent - if isinstance(value, dict): - yaml_str += f"{spaces}{key}:\n{format_yaml_like(value, indent + 1)}" - else: - yaml_str += f"{spaces}{key}: {value}\n" - return yaml_str - -def save_versions(): - """Save Python and pandas versions in YAML-like format.""" - versions = { - "plot_bed.py": { - "python": platform.python_version(), - "pandas": pd.__version__ - } - } - with open("versions.yml", "w") as f: - f.write(format_yaml_like(versions)) - -real_bed_file = sys.argv[1] -benchmarking_bed_file = sys.argv[2] -output_file = sys.argv[3] - -real_data = read_bed(real_bed_file, 'real') -benchmarking_data = read_bed(benchmarking_bed_file, 'benchmarking') - -datasets = [(real_data, 'real'), (benchmarking_data, 'benchmarking')] -plot_bed(datasets, output_file) -save_versions() diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index f6a3e748..48ca68a6 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -37,8 +37,6 @@ workflow BENCHMARKING { benchmarking: meta.benchmarking }.set { ch_merged } - ch_merged.real.view {"emits: $it"} - ch_joined = ch_merged.real.map{ meta, bed -> [[id: meta.tool], bed]} .join(ch_merged.benchmarking.map{ meta, bed -> [[id: meta.tool], bed]}) @@ -68,17 +66,6 @@ workflow BENCHMARKING { ch_path = ch_joined.map { it[1] } ch_corr_inputs = ch_meta.combine(ch_path) - ch_real_bed.combine(ch_depthfile) - .flatMap { bed, depthfile -> - def (meta, bed_path) = bed - [meta, bed_path, depthfile] - } - .set { ch_depth_correlation } - - ch_depth_correlation.collect() - .collectFile(name: 'corr.txt', storeDir: params.outdir, newLine: true) { file -> - file.collect { it.text }.join('\n') - } ch_jaccard = BEDTOOLS_JACCARD(ch_joined, [[], []]).tsv diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 39889edc..69af2a00 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -161,7 +161,7 @@ workflow CIRCRNA_DISCOVERY { annotation_gtf = ANNOTATION.out.gtf counts_bed = MERGE_SAMPLES.out.counts_bed counts_tsv = MERGE_SAMPLES.out.counts_tsv - star_bam = STAR_2ND_PASS.out.bam + star_bam = STAR2PASS.out.bam multiqc_files = ch_multiqc_files versions = ch_versions diff --git a/subworkflows/local/discovery/star2pass.nf b/subworkflows/local/discovery/star2pass.nf index 4e216545..4545c909 100644 --- a/subworkflows/local/discovery/star2pass.nf +++ b/subworkflows/local/discovery/star2pass.nf @@ -29,6 +29,7 @@ workflow STAR2PASS { junction = PASS_2.out.junction sam = PASS_2.out.sam tab = PASS_2.out.tab + bam = PASS_2.out.bam versions = ch_versions } diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 88c4e16c..081a3bd1 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -175,7 +175,6 @@ workflow CIRCRNA { bwa_index, chromosomes, hisat2_index, - segemehl_index, star_index, params.bsj_reads, params.tool_filter, @@ -184,8 +183,8 @@ workflow CIRCRNA { ) BENCHMARKING( - CIRCRNA_DISCOVERY.out.tool_bed, - CIRCRNA_DISCOVERY_BENCHMARKING.out.tool_bed, + CIRCRNA_DISCOVERY.out.annotation_bed, + CIRCRNA_DISCOVERY_BENCHMARKING.out.annotation_bed, CIRCRNA_DISCOVERY.out.star_bam, CIRCRNA_DISCOVERY_BENCHMARKING.out.star_bam, FASTQC_TRIMGALORE.out.trim_log From 7e6a94467894731cdd1963876f216ee2b1d9d249 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Sat, 22 Jun 2024 12:00:18 +0200 Subject: [PATCH 13/32] diagnostic: comparison to older version needed --- .../local/benchmarking/seq_depth_plot/main.nf | 5 +++- subworkflows/local/benchmarking.nf | 24 ++++++++++++------- 2 files changed, 20 insertions(+), 9 deletions(-) diff --git a/modules/local/benchmarking/seq_depth_plot/main.nf b/modules/local/benchmarking/seq_depth_plot/main.nf index 17e130b9..d3470a73 100644 --- a/modules/local/benchmarking/seq_depth_plot/main.nf +++ b/modules/local/benchmarking/seq_depth_plot/main.nf @@ -5,7 +5,10 @@ process SEQ_DEPTH_CORRELLATION { container 'https://depot.galaxyproject.org/singularity/bionumpy:0.2.12--pyha8f3691_0' input: - tuple val(meta), path(bed), path(depth) + tuple val(meta), + path(bed) + tuple val(depth_meta), + path(depth) output: path("*.txt") , emit: report script: diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index 48ca68a6..37827196 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -30,22 +30,35 @@ workflow BENCHMARKING { benchmarking: meta.benchmarking], bed]} .groupTuple() + ch_all.view {"all: $it"} + SORT(ch_all) + SORT.out.sorted.view { "sort: $it"} + BEDTOOLS_MERGE(SORT.out.sorted).bed.branch{ meta, bed -> real: !meta.benchmarking benchmarking: meta.benchmarking }.set { ch_merged } + ch_merged.real.view { "merged_rea: $it" } + + ch_merged.benchmarking.view { "merged_ben: $it" } + ch_joined = ch_merged.real.map{ meta, bed -> [[id: meta.tool], bed]} .join(ch_merged.benchmarking.map{ meta, bed -> [[id: meta.tool], bed]}) + ch_joined.view { "joined1: $it"} ch_intersect = BEDTOOLS_INTERSECT(ch_joined,[[], []]) OVERLAP_PLOT(ch_intersect) + ch_joined.view { "joined2: $it"} + LOCATION_PLOT(ch_joined) + ch_joined.view { "joined3: $it"} + ch_meta = ch_real_bam.map { it[0] } ch_path = ch_real_bam.map { it[1] } ch_scale = Channel.value(1) @@ -56,15 +69,10 @@ workflow BENCHMARKING { ch_genomecov = BEDTOOLS_GENOMECOV(ch_genomecov_inputs, [], "bg",false) - ch_depthfile = WRITE(ch_genomecov.genomecov).flatten() - .collectFile(storeDir: params.outdir, newLine: true) { file -> - def content = file.text - return ['genomecovs.txt', content] - } + ch_joined.view { "joined: $it"} - ch_meta = ch_joined.map { it[0] } - ch_path = ch_joined.map { it[1] } - ch_corr_inputs = ch_meta.combine(ch_path) + ch_corr = SEQ_DEPTH_CORRELLATION(ch_joined, ch_genomecov.genomecov) + ch_corr.view { "emits: $it"} ch_jaccard = BEDTOOLS_JACCARD(ch_joined, [[], []]).tsv From 4a064262b2c081340cd3e33aafe835978654f3a1 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Mon, 24 Jun 2024 17:46:02 +0200 Subject: [PATCH 14/32] Fixed benchmarking.nf input to be tool specific as previously. Fixed Pearson-correllation. Implemented collection of correlation values. --- .../local/benchmarking/seq_depth_plot/main.nf | 2 +- .../seq_depth_plot/templates/create_plots.py | 24 ++++---------- subworkflows/local/benchmarking.nf | 32 +++++++++++-------- subworkflows/local/circrna_discovery.nf | 6 +++- workflows/circrna/main.nf | 4 +-- 5 files changed, 33 insertions(+), 35 deletions(-) diff --git a/modules/local/benchmarking/seq_depth_plot/main.nf b/modules/local/benchmarking/seq_depth_plot/main.nf index d3470a73..f397bdab 100644 --- a/modules/local/benchmarking/seq_depth_plot/main.nf +++ b/modules/local/benchmarking/seq_depth_plot/main.nf @@ -10,7 +10,7 @@ process SEQ_DEPTH_CORRELLATION { tuple val(depth_meta), path(depth) output: - path("*.txt") , emit: report + path("*.tsv") , emit: report script: template "create_plots.py" } \ No newline at end of file diff --git a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py index d868c739..c9a492ae 100644 --- a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py +++ b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py @@ -9,17 +9,6 @@ depth = "$depth" bed = "$bed" -def extract_matching_paths(array, filepath): - array_id = array.split(",")[0].split(":")[1] - matching_paths = [] - with open(filepath, 'r') as file: - for line in file: - line_id = line.split(",")[0].split(":")[1] - if array_id == line_id: - path = line.split()[-1] - matching_paths.append(path) - return matching_paths - def calculate_correlation(bed_file_path, depth_file_path): # Read the BED file and store circRNA regions circRNA_regions = [] @@ -62,9 +51,10 @@ def calculate_correlation(bed_file_path, depth_file_path): return correlation -with open('stats.txt', 'w') as outfile: - for path in extract_matching_paths(meta, depth): - corr = calculate_correlation(bed, path) - output_line = meta.split(",")[3] + ' ' + str(corr) - outfile.write(output_line) - logging.debug(f'Written to stats.txt: {output_line.strip()}') +# Calculate correlation using the provided bed and depth files +corr = calculate_correlation(bed, depth) + +header = "tool\\tpearson_corr\\n" +# Write the correlation to stats.txt +with open('stats.tsv', 'w') as outfile: + outfile.write(header + meta.split(",")[4][:-1] + '\\t' + str(corr)) diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index 37827196..96de06f7 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -10,6 +10,8 @@ include { SEQ_DEPTH_CORRELLATION} from '../../modules/local/benchmarking/seq_dep include { WRITE } from '../../modules/local/benchmarking/write_file' include { WRITE as WRITE2 } from '../../modules/local/benchmarking/write_file' +import groovy.json.JsonSlurper + workflow BENCHMARKING { @@ -22,6 +24,8 @@ workflow BENCHMARKING { main: + ch_real_bed.view{"real:$it}"} + ch_versions = Channel.empty() ch_all = ch_real_bed.mix(ch_benchmarking_bed) @@ -30,34 +34,24 @@ workflow BENCHMARKING { benchmarking: meta.benchmarking], bed]} .groupTuple() - ch_all.view {"all: $it"} SORT(ch_all) - SORT.out.sorted.view { "sort: $it"} - BEDTOOLS_MERGE(SORT.out.sorted).bed.branch{ meta, bed -> real: !meta.benchmarking benchmarking: meta.benchmarking }.set { ch_merged } - ch_merged.real.view { "merged_rea: $it" } - - ch_merged.benchmarking.view { "merged_ben: $it" } - ch_joined = ch_merged.real.map{ meta, bed -> [[id: meta.tool], bed]} .join(ch_merged.benchmarking.map{ meta, bed -> [[id: meta.tool], bed]}) - ch_joined.view { "joined1: $it"} ch_intersect = BEDTOOLS_INTERSECT(ch_joined,[[], []]) OVERLAP_PLOT(ch_intersect) - ch_joined.view { "joined2: $it"} - LOCATION_PLOT(ch_joined) - ch_joined.view { "joined3: $it"} + ch_real_bam.view {"bam: $it"} ch_meta = ch_real_bam.map { it[0] } ch_path = ch_real_bam.map { it[1] } @@ -69,14 +63,22 @@ workflow BENCHMARKING { ch_genomecov = BEDTOOLS_GENOMECOV(ch_genomecov_inputs, [], "bg",false) - ch_joined.view { "joined: $it"} + ch_corr = SEQ_DEPTH_CORRELLATION(ch_real_bed, ch_genomecov.genomecov) - ch_corr = SEQ_DEPTH_CORRELLATION(ch_joined, ch_genomecov.genomecov) - ch_corr.view { "emits: $it"} + ch_pearson = ch_corr.splitCsv(header: true, sep: "\t") + .map{ values -> [values.tool, values.pearson_corr]} + .collectFile( newLine: true, + storeDir: params.outdir, + seed: "tool\tpearson_corr") { + row -> ["pearson.tsv", row.join("\t")] + } + ch_pearson.view { "pearson: $it" } ch_jaccard = BEDTOOLS_JACCARD(ch_joined, [[], []]).tsv + ch_jaccard.view { "jaccard: $it" } + ch_stats = ch_jaccard.splitCsv(header: true, sep: "\t") .map{ meta, values -> [meta.id, values.intersection, values.union, values.jaccard, values.n_intersections]} .collectFile( newLine: true, @@ -85,6 +87,8 @@ workflow BENCHMARKING { row -> ["jaccard.tsv", row.join("\t")] } + ch_stats.view {"stats: $it"} + BENCHMARKING_MULTIQC(ch_stats) ch_versions = ch_versions.mix(SORT.out.versions) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 69af2a00..5f3c2513 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -154,6 +154,9 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(BEDTOOLS_GETFASTA.out.versions) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) + + + emit: tool_bed = ANNOTATION.out.merged_bed fasta = ADD_BACKSPLICE.out.output @@ -161,7 +164,8 @@ workflow CIRCRNA_DISCOVERY { annotation_gtf = ANNOTATION.out.gtf counts_bed = MERGE_SAMPLES.out.counts_bed counts_tsv = MERGE_SAMPLES.out.counts_tsv - star_bam = STAR2PASS.out.bam + star_bam = STAR2PASS.out.bam + tool_bed = ch_bed multiqc_files = ch_multiqc_files versions = ch_versions diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 081a3bd1..44e9a565 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -183,8 +183,8 @@ workflow CIRCRNA { ) BENCHMARKING( - CIRCRNA_DISCOVERY.out.annotation_bed, - CIRCRNA_DISCOVERY_BENCHMARKING.out.annotation_bed, + CIRCRNA_DISCOVERY.out.tool_bed, + CIRCRNA_DISCOVERY_BENCHMARKING.out.tool_bed, CIRCRNA_DISCOVERY.out.star_bam, CIRCRNA_DISCOVERY_BENCHMARKING.out.star_bam, FASTQC_TRIMGALORE.out.trim_log From 931698db2cd9cdef4353410d8e3d5ef8c002b470 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Tue, 25 Jun 2024 12:26:51 +0200 Subject: [PATCH 15/32] added sequence depth to mulitiqc. Changed labels and layout of location plots --- .../local/benchmarking/average_tsv/main.nf | 18 +++++++ .../average_tsv/templates/average.py | 13 +++++ .../location_plots/templates/create_plots.py | 54 ++++++++----------- .../seq_depth_plot/templates/create_plots.py | 8 ++- subworkflows/local/benchmarking.nf | 29 +++++----- 5 files changed, 69 insertions(+), 53 deletions(-) create mode 100644 modules/local/benchmarking/average_tsv/main.nf create mode 100644 modules/local/benchmarking/average_tsv/templates/average.py diff --git a/modules/local/benchmarking/average_tsv/main.nf b/modules/local/benchmarking/average_tsv/main.nf new file mode 100644 index 00000000..bc16ee6d --- /dev/null +++ b/modules/local/benchmarking/average_tsv/main.nf @@ -0,0 +1,18 @@ +process AVERGAGE_TSV { + label "process_single" + + conda "bioconda::pandas=1.5.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'biocontainers/pandas:1.5.2' }" + + + input: + path(tsv) + + output: + path(tsv) + + script: + template "average.py" +} diff --git a/modules/local/benchmarking/average_tsv/templates/average.py b/modules/local/benchmarking/average_tsv/templates/average.py new file mode 100644 index 00000000..b749366d --- /dev/null +++ b/modules/local/benchmarking/average_tsv/templates/average.py @@ -0,0 +1,13 @@ +#!/usr/bin/env python3 + +import pandas as pd + +tsv = "$tsv" +data = pd.read_csv(tsv, sep='\t') + +data['tool'] = data['tool'].str.replace('tool:', '') +average_values = data.groupby('tool')['pearson_corr'].mean().reset_index() + +output_file_path = tsv +average_values.to_csv(output_file_path, sep='\t', index=False) + diff --git a/modules/local/benchmarking/location_plots/templates/create_plots.py b/modules/local/benchmarking/location_plots/templates/create_plots.py index 265e4605..c803a39e 100755 --- a/modules/local/benchmarking/location_plots/templates/create_plots.py +++ b/modules/local/benchmarking/location_plots/templates/create_plots.py @@ -42,33 +42,30 @@ def combine_data(data1, data2): 'File Label': combined_data['file_label'] }) -# Combine File Label and Strand into a single column for easier plotting -df['File_Strand'] = df['File Label'] + ' ' + df['Strand'] - -# Separate the data by strand -df_plus = df[df['Strand'] == '+'] -df_minus = df[df['Strand'] == '-'] +# Separate the data by file label +df_real = df[df['File Label'] == 'real'] +df_benchmark = df[df['File Label'] == 'benchmark'] # Create figure and axes fig, ax = plt.subplots(figsize=(12, 6)) # Define the color palette -palette_plus = { - "real +": "red", - "benchmark +": "blue" +palette_real = { + "+": "red", + "-": "lightcoral" } -palette_minus = { - "real -": "lightcoral", - "benchmark -": "lightblue" +palette_benchmark = { + "+": "blue", + "-": "lightblue" } -# Draw violins for the + strand +# Draw violins for the real file sns.violinplot( x="Chromosome", y="Start Location", - hue="File_Strand", - data=df_plus, - palette=palette_plus, + hue="Strand", + data=df_real, + palette=palette_real, split=True, ax=ax, scale="count", @@ -77,13 +74,13 @@ def combine_data(data1, data2): inner=None ) -# Draw violins for the - strand +# Draw violins for the benchmark file sns.violinplot( x="Chromosome", y="Start Location", - hue="File_Strand", - data=df_minus, - palette=palette_minus, + hue="Strand", + data=df_benchmark, + palette=palette_benchmark, split=True, ax=ax, scale="count", @@ -98,21 +95,14 @@ def combine_data(data1, data2): # Compose a custom legend custom_lines = [ - Line2D([0], [0], color=color, lw=4, alpha=0.25) - for color in palette_plus.values() -] + [ - Line2D([0], [0], color=color, lw=4, alpha=0.25) - for color in palette_minus.values() + Line2D([0], [0], color=palette_real["+"], lw=4, alpha=0.25), + Line2D([0], [0], color=palette_real["-"], lw=4, alpha=0.25), + Line2D([0], [0], color=palette_benchmark["+"], lw=4, alpha=0.25), + Line2D([0], [0], color=palette_benchmark["-"], lw=4, alpha=0.25) ] -ax.legend( - custom_lines, - list(palette_plus.keys()) + list(palette_minus.keys()), - title="File : Strand" -) +ax.legend(custom_lines, ["Total +", "Total -", "PolyA +", "PolyA -"], title="File : Strand") plt.title('Start Locations of circRNA by Chromosome and Strand') plot_file_name = f"{input_bed_file_1.replace('.bed','')}_{input_bed_file_2.replace('.bed','')}_mqc.png" # Save the plot plt.savefig(plot_file_name, bbox_inches='tight') - - diff --git a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py index c9a492ae..059e2372 100644 --- a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py +++ b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py @@ -2,9 +2,6 @@ import logging import numpy as np -# Initialize logging -logging.basicConfig(filename='process_log.log', level=logging.DEBUG, format='%(asctime)s - %(levelname)s - %(message)s') - meta = "$meta" depth = "$depth" bed = "$bed" @@ -54,7 +51,8 @@ def calculate_correlation(bed_file_path, depth_file_path): # Calculate correlation using the provided bed and depth files corr = calculate_correlation(bed, depth) -header = "tool\\tpearson_corr\\n" + # Write the correlation to stats.txt -with open('stats.tsv', 'w') as outfile: +with open('corr_mqc.tsv', 'w') as outfile: + header = "tool\\tpearson_corr\\n" outfile.write(header + meta.split(",")[4][:-1] + '\\t' + str(corr)) diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index 96de06f7..db11022d 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -3,14 +3,13 @@ include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge' include { BEDTOOLS_INTERSECT } from '../../modules/nf-core/bedtools/intersect' include { BEDTOOLS_JACCARD } from '../../modules/nf-core/bedtools/jaccard' include { BEDTOOLS_GENOMECOV } from '../../modules/nf-core/bedtools/genomecov' -include { BENCHMARKING_MULTIQC } from '../../modules/local/benchmarking/multiqc' +include { BENCHMARKING_MULTIQC as JACCARD_MULTIQC } from '../../modules/local/benchmarking/multiqc' +include { BENCHMARKING_MULTIQC as CORRELATION_MULTIQC } from '../../modules/local/benchmarking/multiqc' include { LOCATION_PLOT } from '../../modules/local/benchmarking/location_plots' include { OVERLAP_PLOT } from '../../modules/local/benchmarking/overlap_plot' include { SEQ_DEPTH_CORRELLATION} from '../../modules/local/benchmarking/seq_depth_plot' -include { WRITE } from '../../modules/local/benchmarking/write_file' -include { WRITE as WRITE2 } from '../../modules/local/benchmarking/write_file' +include { AVERGAGE_TSV } from '../../modules/local/benchmarking/average_tsv' -import groovy.json.JsonSlurper workflow BENCHMARKING { @@ -24,8 +23,6 @@ workflow BENCHMARKING { main: - ch_real_bed.view{"real:$it}"} - ch_versions = Channel.empty() ch_all = ch_real_bed.mix(ch_benchmarking_bed) @@ -51,8 +48,6 @@ workflow BENCHMARKING { LOCATION_PLOT(ch_joined) - ch_real_bam.view {"bam: $it"} - ch_meta = ch_real_bam.map { it[0] } ch_path = ch_real_bam.map { it[1] } ch_scale = Channel.value(1) @@ -73,11 +68,13 @@ workflow BENCHMARKING { row -> ["pearson.tsv", row.join("\t")] } - ch_pearson.view { "pearson: $it" } + AVERGAGE_TSV(ch_pearson) + CORRELATION_MULTIQC(AVERGAGE_TSV.out) - ch_jaccard = BEDTOOLS_JACCARD(ch_joined, [[], []]).tsv + CORRELATION_MULTIQC.out.report.view {"emits: $it"} - ch_jaccard.view { "jaccard: $it" } + + ch_jaccard = BEDTOOLS_JACCARD(ch_joined, [[], []]).tsv ch_stats = ch_jaccard.splitCsv(header: true, sep: "\t") .map{ meta, values -> [meta.id, values.intersection, values.union, values.jaccard, values.n_intersections]} @@ -87,17 +84,17 @@ workflow BENCHMARKING { row -> ["jaccard.tsv", row.join("\t")] } - ch_stats.view {"stats: $it"} - - BENCHMARKING_MULTIQC(ch_stats) + JACCARD_MULTIQC(ch_stats) ch_versions = ch_versions.mix(SORT.out.versions) ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) ch_versions = ch_versions.mix(BEDTOOLS_JACCARD.out.versions) - ch_versions = ch_versions.mix(BENCHMARKING_MULTIQC.out.versions) + ch_versions = ch_versions.mix(JACCARD_MULTIQC.out.versions) + ch_versions = ch_versions.mix(CORRELATION_MULTIQC.out.versions) - ch_reports = BENCHMARKING_MULTIQC.out.report.mix(LOCATION_PLOT.out.report) + ch_reports = JACCARD_MULTIQC.out.report.mix(LOCATION_PLOT.out.report) ch_reports = ch_reports.mix(OVERLAP_PLOT.out.report) + ch_reports = ch_reports.mix(CORRELATION_MULTIQC.out.report) emit: reports = ch_reports From 5bb7aa9453fe395452b6ba222ca2c337f3ac5771 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Tue, 25 Jun 2024 12:46:11 +0200 Subject: [PATCH 16/32] pre-commit run pass. Deleted redundant module --- assets/multiqc_config.yml | 1 - modules.json | 102 +++++------------- .../local/benchmarking/average_tsv/main.nf | 4 +- .../local/benchmarking/location_plots/main.nf | 4 +- .../location_plots/templates/create_plots.py | 12 +-- modules/local/benchmarking/multiqc/main.nf | 6 +- .../multiqc/templates/benchmarking.py | 2 +- .../local/benchmarking/overlap_plot/main.nf | 4 +- .../local/benchmarking/seq_depth_plot/main.nf | 4 +- .../seq_depth_plot/templates/create_plots.py | 20 ++-- modules/local/benchmarking/write_file/main.nf | 13 --- .../write_file/templates/write.py | 11 -- nextflow_schema.json | 21 +--- subworkflows/local/benchmarking.nf | 2 +- 14 files changed, 59 insertions(+), 147 deletions(-) delete mode 100644 modules/local/benchmarking/write_file/main.nf delete mode 100644 modules/local/benchmarking/write_file/templates/write.py diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 34963d4a..e5337fdc 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -11,7 +11,6 @@ report_section_order: order: -1002 "nf-core-circrna-summary": order: -1003 - export_plots: true diff --git a/modules.json b/modules.json index ca3e3065..4a427bf7 100644 --- a/modules.json +++ b/modules.json @@ -8,9 +8,7 @@ "bedtools/genomecov": { "branch": "master", "git_sha": "81b90194ce9911dbd55bba2c65c6919f6677abc4", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/getfasta": { "branch": "master", @@ -20,44 +18,32 @@ "bedtools/intersect": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/jaccard": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/merge": { "branch": "master", "git_sha": "a5377837fe9013bde89de8689829e83e84086536", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bowtie/align": { "branch": "master", "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bowtie/build": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bowtie2/align": { "branch": "master", @@ -67,9 +53,7 @@ "bowtie2/build": { "branch": "master", "git_sha": "1fea64f5132a813ec97c1c6d3a74e0aee7142b6d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/index": { "branch": "master", @@ -79,9 +63,7 @@ "cat/cat": { "branch": "master", "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", @@ -91,16 +73,12 @@ "circexplorer2/annotate": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "circexplorer2/parse": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "csvtk/join": { "branch": "master", @@ -115,16 +93,12 @@ "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/tx2gene": { "branch": "master", "git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", @@ -144,37 +118,27 @@ "hisat2/align": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hisat2/build": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hisat2/extractsplicesites": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "miranda": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", @@ -219,37 +183,27 @@ "segemehl/index": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "star/align": { "branch": "master", "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "stringtie/stringtie": { "branch": "master", "git_sha": "b1b959609bda44341120aed1766329909f54b8d0", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "trimgalore": { "branch": "master", "git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tximeta/tximport": { "branch": "master", @@ -273,9 +227,7 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", @@ -285,12 +237,10 @@ "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} diff --git a/modules/local/benchmarking/average_tsv/main.nf b/modules/local/benchmarking/average_tsv/main.nf index bc16ee6d..fe4cac93 100644 --- a/modules/local/benchmarking/average_tsv/main.nf +++ b/modules/local/benchmarking/average_tsv/main.nf @@ -9,10 +9,10 @@ process AVERGAGE_TSV { input: path(tsv) - + output: path(tsv) - + script: template "average.py" } diff --git a/modules/local/benchmarking/location_plots/main.nf b/modules/local/benchmarking/location_plots/main.nf index fa3e3932..45be3ab5 100644 --- a/modules/local/benchmarking/location_plots/main.nf +++ b/modules/local/benchmarking/location_plots/main.nf @@ -7,7 +7,7 @@ process LOCATION_PLOT { input: tuple val(id), path(bedfile1), path(bedfile2) output: - path("*_mqc.png") , emit: report + path("*_mqc.png") , emit: report script: template "create_plots.py" -} \ No newline at end of file +} diff --git a/modules/local/benchmarking/location_plots/templates/create_plots.py b/modules/local/benchmarking/location_plots/templates/create_plots.py index c803a39e..d5e589e1 100755 --- a/modules/local/benchmarking/location_plots/templates/create_plots.py +++ b/modules/local/benchmarking/location_plots/templates/create_plots.py @@ -51,18 +51,18 @@ def combine_data(data1, data2): # Define the color palette palette_real = { - "+": "red", + "+": "red", "-": "lightcoral" } palette_benchmark = { - "+": "blue", + "+": "blue", "-": "lightblue" } # Draw violins for the real file sns.violinplot( - x="Chromosome", - y="Start Location", + x="Chromosome", + y="Start Location", hue="Strand", data=df_real, palette=palette_real, @@ -76,8 +76,8 @@ def combine_data(data1, data2): # Draw violins for the benchmark file sns.violinplot( - x="Chromosome", - y="Start Location", + x="Chromosome", + y="Start Location", hue="Strand", data=df_benchmark, palette=palette_benchmark, diff --git a/modules/local/benchmarking/multiqc/main.nf b/modules/local/benchmarking/multiqc/main.nf index 4a366383..a39675d3 100644 --- a/modules/local/benchmarking/multiqc/main.nf +++ b/modules/local/benchmarking/multiqc/main.nf @@ -8,11 +8,11 @@ process BENCHMARKING_MULTIQC { input: path(jaccard) - + output: path("*_mqc.json") , emit: report path("versions.yml"), emit: versions - + script: template "benchmarking.py" -} \ No newline at end of file +} diff --git a/modules/local/benchmarking/multiqc/templates/benchmarking.py b/modules/local/benchmarking/multiqc/templates/benchmarking.py index fa1fe401..1515e819 100644 --- a/modules/local/benchmarking/multiqc/templates/benchmarking.py +++ b/modules/local/benchmarking/multiqc/templates/benchmarking.py @@ -47,4 +47,4 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: } } with open("versions.yml", "w") as f: - f.write(format_yaml_like(versions)) \ No newline at end of file + f.write(format_yaml_like(versions)) diff --git a/modules/local/benchmarking/overlap_plot/main.nf b/modules/local/benchmarking/overlap_plot/main.nf index 0315b575..b016b53b 100644 --- a/modules/local/benchmarking/overlap_plot/main.nf +++ b/modules/local/benchmarking/overlap_plot/main.nf @@ -8,7 +8,7 @@ process OVERLAP_PLOT { tuple val(meta), path(bed) path "versions.yml" output: - path("*_mqc.png") , emit: report + path("*_mqc.png") , emit: report script: template "create_plots.py" -} \ No newline at end of file +} diff --git a/modules/local/benchmarking/seq_depth_plot/main.nf b/modules/local/benchmarking/seq_depth_plot/main.nf index f397bdab..c69a1af8 100644 --- a/modules/local/benchmarking/seq_depth_plot/main.nf +++ b/modules/local/benchmarking/seq_depth_plot/main.nf @@ -10,7 +10,7 @@ process SEQ_DEPTH_CORRELLATION { tuple val(depth_meta), path(depth) output: - path("*.tsv") , emit: report + path("*.tsv") , emit: report script: template "create_plots.py" -} \ No newline at end of file +} diff --git a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py index 059e2372..8aa83658 100644 --- a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py +++ b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py @@ -16,36 +16,36 @@ def calculate_correlation(bed_file_path, depth_file_path): start = int(parts[1]) end = int(parts[2]) circRNA_regions.append((chr, start, end)) - + # Read the sequence depth file circRNA_presence = [] sequencing_depth = [] - + with open(depth_file_path, 'r') as depth_file: bed_idx = 0 bed_len = len(circRNA_regions) - + for line in depth_file: parts = line.strip().split() chr = parts[0] pos = int(parts[1]) depth = int(parts[2]) - + # Move bed_idx to the correct region while bed_idx < bed_len and (circRNA_regions[bed_idx][0] < chr or (circRNA_regions[bed_idx][0] == chr and circRNA_regions[bed_idx][2] < pos)): bed_idx += 1 - + # Check if the current position is within a circRNA region if bed_idx < bed_len and circRNA_regions[bed_idx][0] == chr and circRNA_regions[bed_idx][1] <= pos <= circRNA_regions[bed_idx][2]: circRNA_presence.append(1) else: circRNA_presence.append(0) - + sequencing_depth.append(depth) - + # Calculate the correlation coefficient correlation = np.corrcoef(sequencing_depth, circRNA_presence)[0, 1] - + return correlation # Calculate correlation using the provided bed and depth files @@ -53,6 +53,6 @@ def calculate_correlation(bed_file_path, depth_file_path): # Write the correlation to stats.txt -with open('corr_mqc.tsv', 'w') as outfile: - header = "tool\\tpearson_corr\\n" +with open('corr_mqc.tsv', 'w') as outfile: + header = "tool\\tpearson_corr\\n" outfile.write(header + meta.split(",")[4][:-1] + '\\t' + str(corr)) diff --git a/modules/local/benchmarking/write_file/main.nf b/modules/local/benchmarking/write_file/main.nf deleted file mode 100644 index 317ae47a..00000000 --- a/modules/local/benchmarking/write_file/main.nf +++ /dev/null @@ -1,13 +0,0 @@ -process WRITE { - label "process_single" - - conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2" - container 'uphl/seaborn' - - input: - tuple val(meta), path(value) - output: - path("*.txt") , optional:true, emit: report - script: - template "write.py" -} \ No newline at end of file diff --git a/modules/local/benchmarking/write_file/templates/write.py b/modules/local/benchmarking/write_file/templates/write.py deleted file mode 100644 index 7772556d..00000000 --- a/modules/local/benchmarking/write_file/templates/write.py +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/env python3 -import os -m = "$meta" -v = "$value" - - -with open("output.txt", "w") as file: - # Write the variables to the file - v = os.path.abspath(v) - file.write(m + '\t') - file.write(v) \ No newline at end of file diff --git a/nextflow_schema.json b/nextflow_schema.json index 91ff3329..1bc3f1f1 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,10 +10,7 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": [ - "input", - "outdir" - ], + "required": ["input", "outdir"], "properties": { "input": { "type": "string", @@ -94,10 +91,7 @@ "fa_icon": "fas fa-copy", "description": "Aggregate function to apply to duplicate circRNAs when more than one quantification tool has been selected. Options: max, mean", "default": "mean", - "enum": [ - "mean", - "max" - ] + "enum": ["mean", "max"] }, "save_intermediates": { "type": "boolean", @@ -466,14 +460,7 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": [ - "symlink", - "rellink", - "link", - "copy", - "copyNoFollow", - "move" - ], + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "hidden": true }, "email": { @@ -598,4 +585,4 @@ "$ref": "#/definitions/generic_options" } ] -} \ No newline at end of file +} diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index db11022d..420bc989 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -99,4 +99,4 @@ workflow BENCHMARKING { emit: reports = ch_reports versions = ch_versions // channel: [ versions.yml ] -} \ No newline at end of file +} From 1e12d20ada96ca8f17af0f57c79d968865dfb9d3 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Wed, 26 Jun 2024 21:18:47 +0200 Subject: [PATCH 17/32] Added sections to multiqc, fixed an issue where the Seq-depth-correlation was calculated from the wrong files --- .../local/benchmarking/location_plots/main.nf | 2 +- modules/local/benchmarking/png_json/main.nf | 19 +++++++++ .../benchmarking/png_json/templates/json.py | 40 +++++++++++++++++++ .../local/benchmarking/seq_depth_plot/main.nf | 1 - .../seq_depth_plot/templates/create_plots.py | 23 +++++++---- subworkflows/local/benchmarking.nf | 36 ++++++++++------- 6 files changed, 97 insertions(+), 24 deletions(-) create mode 100644 modules/local/benchmarking/png_json/main.nf create mode 100644 modules/local/benchmarking/png_json/templates/json.py diff --git a/modules/local/benchmarking/location_plots/main.nf b/modules/local/benchmarking/location_plots/main.nf index 45be3ab5..fff9da68 100644 --- a/modules/local/benchmarking/location_plots/main.nf +++ b/modules/local/benchmarking/location_plots/main.nf @@ -7,7 +7,7 @@ process LOCATION_PLOT { input: tuple val(id), path(bedfile1), path(bedfile2) output: - path("*_mqc.png") , emit: report + path("*_mqc.png") script: template "create_plots.py" } diff --git a/modules/local/benchmarking/png_json/main.nf b/modules/local/benchmarking/png_json/main.nf new file mode 100644 index 00000000..fab4be69 --- /dev/null +++ b/modules/local/benchmarking/png_json/main.nf @@ -0,0 +1,19 @@ +process PNG_JSON { + label "process_single" + + conda "bioconda::pandas=1.5.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'biocontainers/pandas:1.5.2' }" + + input: + path(png) + val(title) + val(description) + + output: + path("*_mqc.json") , emit: report + + script: + template "json.py" +} diff --git a/modules/local/benchmarking/png_json/templates/json.py b/modules/local/benchmarking/png_json/templates/json.py new file mode 100644 index 00000000..1f16f43b --- /dev/null +++ b/modules/local/benchmarking/png_json/templates/json.py @@ -0,0 +1,40 @@ +#!/usr/bin/env python3 + +import json +import os +import base64 + +# Assuming these variables are set properly in your environment or script +png = "$png" +title = "$title" +description = "$description" + +# Ensure the png path is an absolute path +absolute_path = os.path.abspath(png) + +filename = os.path.basename(absolute_path) +name = filename.rstrip("_mcq.png") + +id = title.lower().replace(" ", "_") + +# Convert the PNG file to a base64 string +with open(absolute_path, "rb") as image_file: + base64_string = base64.b64encode(image_file.read()).decode('utf-8') + +# Create the data structure for JSON +data = { + "id": f"benchmarking_{name}", + "parent_id": id, + "parent_name": title, + "parent_description": description, + "section_name": name, + "plot_type": "image", + "data": f'
' +} + +# Write the JSON data to a file +with open(f"{name}_mqc.json", "w") as f: + json.dump(data, f, indent=4) + +print(f"JSON file created for {absolute_path}") + diff --git a/modules/local/benchmarking/seq_depth_plot/main.nf b/modules/local/benchmarking/seq_depth_plot/main.nf index c69a1af8..f147a1a7 100644 --- a/modules/local/benchmarking/seq_depth_plot/main.nf +++ b/modules/local/benchmarking/seq_depth_plot/main.nf @@ -7,7 +7,6 @@ process SEQ_DEPTH_CORRELLATION { input: tuple val(meta), path(bed) - tuple val(depth_meta), path(depth) output: path("*.tsv") , emit: report diff --git a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py index 8aa83658..4a69874a 100644 --- a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py +++ b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py @@ -1,5 +1,6 @@ #!/usr/bin/env python3 -import logging +import os +import re import numpy as np meta = "$meta" @@ -48,11 +49,17 @@ def calculate_correlation(bed_file_path, depth_file_path): return correlation -# Calculate correlation using the provided bed and depth files -corr = calculate_correlation(bed, depth) +id = re.search(r'id:(\\w+)', meta).group(1) - -# Write the correlation to stats.txt -with open('corr_mqc.tsv', 'w') as outfile: - header = "tool\\tpearson_corr\\n" - outfile.write(header + meta.split(",")[4][:-1] + '\\t' + str(corr)) +with open(depth, 'r') as paths: + for path in paths: + path = path.strip() + basename = os.path.splitext(os.path.basename(path))[0] + + if basename == id: + # Calculate correlation using the provided bed and depth files + corr = calculate_correlation(bed, path) + # Write the correlation to stats.txt + with open('corr_mqc.tsv', 'w') as outfile: + header = "tool\\tpearson_corr\\n" + outfile.write(header + meta.split(",")[4][:-1] + '\\t' + str(corr)) diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index 420bc989..3f25857d 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -1,14 +1,16 @@ -include { GNU_SORT as SORT } from '../../modules/nf-core/gnu/sort' -include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge' -include { BEDTOOLS_INTERSECT } from '../../modules/nf-core/bedtools/intersect' -include { BEDTOOLS_JACCARD } from '../../modules/nf-core/bedtools/jaccard' -include { BEDTOOLS_GENOMECOV } from '../../modules/nf-core/bedtools/genomecov' +include { GNU_SORT as SORT } from '../../modules/nf-core/gnu/sort' +include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge' +include { BEDTOOLS_INTERSECT } from '../../modules/nf-core/bedtools/intersect' +include { BEDTOOLS_JACCARD } from '../../modules/nf-core/bedtools/jaccard' +include { BEDTOOLS_GENOMECOV } from '../../modules/nf-core/bedtools/genomecov' include { BENCHMARKING_MULTIQC as JACCARD_MULTIQC } from '../../modules/local/benchmarking/multiqc' include { BENCHMARKING_MULTIQC as CORRELATION_MULTIQC } from '../../modules/local/benchmarking/multiqc' -include { LOCATION_PLOT } from '../../modules/local/benchmarking/location_plots' -include { OVERLAP_PLOT } from '../../modules/local/benchmarking/overlap_plot' -include { SEQ_DEPTH_CORRELLATION} from '../../modules/local/benchmarking/seq_depth_plot' -include { AVERGAGE_TSV } from '../../modules/local/benchmarking/average_tsv' +include { PNG_JSON as LOCATION_JSON } from '../../modules/local/benchmarking/png_json' +include { PNG_JSON as OVERLAP_JSON } from '../../modules/local/benchmarking/png_json' +include { LOCATION_PLOT } from '../../modules/local/benchmarking/location_plots' +include { OVERLAP_PLOT } from '../../modules/local/benchmarking/overlap_plot' +include { SEQ_DEPTH_CORRELLATION } from '../../modules/local/benchmarking/seq_depth_plot' +include { AVERGAGE_TSV } from '../../modules/local/benchmarking/average_tsv' @@ -45,8 +47,10 @@ workflow BENCHMARKING { ch_intersect = BEDTOOLS_INTERSECT(ch_joined,[[], []]) OVERLAP_PLOT(ch_intersect) + OVERLAP_JSON(OVERLAP_PLOT.out, "Overlap plots", "Plot the overlap circRNAs found in total and polyA data for the tools") LOCATION_PLOT(ch_joined) + LOCATION_JSON(LOCATION_PLOT.out, "Location plots", "Plots the location of the circRNAs found" ) ch_meta = ch_real_bam.map { it[0] } ch_path = ch_real_bam.map { it[1] } @@ -58,7 +62,13 @@ workflow BENCHMARKING { ch_genomecov = BEDTOOLS_GENOMECOV(ch_genomecov_inputs, [], "bg",false) - ch_corr = SEQ_DEPTH_CORRELLATION(ch_real_bed, ch_genomecov.genomecov) + ch_seqdepths = ch_genomecov.genomecov + .map { genomecov_result -> genomecov_result[1].toString() } + .collectFile(name: 'genomecov_paths.txt', + + newLine: true) + + ch_corr = SEQ_DEPTH_CORRELLATION(ch_real_bed, ch_seqdepths.collect()) ch_pearson = ch_corr.splitCsv(header: true, sep: "\t") .map{ values -> [values.tool, values.pearson_corr]} @@ -71,8 +81,6 @@ workflow BENCHMARKING { AVERGAGE_TSV(ch_pearson) CORRELATION_MULTIQC(AVERGAGE_TSV.out) - CORRELATION_MULTIQC.out.report.view {"emits: $it"} - ch_jaccard = BEDTOOLS_JACCARD(ch_joined, [[], []]).tsv @@ -92,8 +100,8 @@ workflow BENCHMARKING { ch_versions = ch_versions.mix(JACCARD_MULTIQC.out.versions) ch_versions = ch_versions.mix(CORRELATION_MULTIQC.out.versions) - ch_reports = JACCARD_MULTIQC.out.report.mix(LOCATION_PLOT.out.report) - ch_reports = ch_reports.mix(OVERLAP_PLOT.out.report) + ch_reports = JACCARD_MULTIQC.out.report.mix(LOCATION_JSON.out.report) + ch_reports = ch_reports.mix(OVERLAP_JSON.out.report) ch_reports = ch_reports.mix(CORRELATION_MULTIQC.out.report) emit: From 0fda391c2ef110d438b430d26477031036f2aa34 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Fri, 28 Jun 2024 11:27:22 +0200 Subject: [PATCH 18/32] Fixed an issue, where the Strands in the multiqc locationplots would sometimes apear the wrong way round --- .../location_plots/templates/create_plots.py | 82 ++++++++----------- .../seq_depth_plot/templates/create_plots.py | 4 +- subworkflows/local/benchmarking.nf | 3 +- 3 files changed, 38 insertions(+), 51 deletions(-) diff --git a/modules/local/benchmarking/location_plots/templates/create_plots.py b/modules/local/benchmarking/location_plots/templates/create_plots.py index d5e589e1..32e63180 100755 --- a/modules/local/benchmarking/location_plots/templates/create_plots.py +++ b/modules/local/benchmarking/location_plots/templates/create_plots.py @@ -19,7 +19,7 @@ def read_bed_file(file_path, label): data['chromosome'].append(row[0]) data['start'].append(int(row[1])) data['strand'].append(row[3]) # Assuming strand information is in the 4th column - data['file_label'].append(label) # Label to indicate the source file + data['file_label'].append(label.lower()) # Label to indicate the source file return data # Combine data function @@ -28,8 +28,8 @@ def combine_data(data1, data2): data1[key].extend(data2[key]) return data1 -data1 = read_bed_file(input_bed_file_1, 'real') -data2 = read_bed_file(input_bed_file_2, 'benchmark') +data1 = read_bed_file(input_bed_file_1, 'total') +data2 = read_bed_file(input_bed_file_2, 'polya') # Combine the two datasets combined_data = combine_data(data1, data2) @@ -42,52 +42,35 @@ def combine_data(data1, data2): 'File Label': combined_data['file_label'] }) -# Separate the data by file label -df_real = df[df['File Label'] == 'real'] -df_benchmark = df[df['File Label'] == 'benchmark'] +# Sort DataFrame to ensure consistent plotting order +df.sort_values(by=['File Label', 'Strand'], inplace=True) # Create figure and axes fig, ax = plt.subplots(figsize=(12, 6)) # Define the color palette -palette_real = { - "+": "red", - "-": "lightcoral" +palette = { + "total +": "red", + "total -": "lightcoral", + "polya +": "blue", + "polya -": "lightblue" } -palette_benchmark = { - "+": "blue", - "-": "lightblue" -} - -# Draw violins for the real file -sns.violinplot( - x="Chromosome", - y="Start Location", - hue="Strand", - data=df_real, - palette=palette_real, - split=True, - ax=ax, - scale="count", - scale_hue=False, - saturation=0.75, - inner=None -) -# Draw violins for the benchmark file -sns.violinplot( - x="Chromosome", - y="Start Location", - hue="Strand", - data=df_benchmark, - palette=palette_benchmark, - split=True, - ax=ax, - scale="count", - scale_hue=False, - saturation=0.75, - inner=None -) +# Draw violins for each file separately +for file_label in df['File Label'].unique(): + sns.violinplot( + x="Chromosome", + y="Start Location", + hue="Strand", + data=df[df['File Label'] == file_label], + palette={"+" : palette[f"{file_label} +"], "-" : palette[f"{file_label} -"]}, + split=True, + ax=ax, + scale="count", + scale_hue=False, + saturation=0.75, + inner=None + ) # Set transparency for all violins for violin in ax.collections: @@ -95,14 +78,19 @@ def combine_data(data1, data2): # Compose a custom legend custom_lines = [ - Line2D([0], [0], color=palette_real["+"], lw=4, alpha=0.25), - Line2D([0], [0], color=palette_real["-"], lw=4, alpha=0.25), - Line2D([0], [0], color=palette_benchmark["+"], lw=4, alpha=0.25), - Line2D([0], [0], color=palette_benchmark["-"], lw=4, alpha=0.25) + Line2D([0], [0], color=palette[f"{file} {strand}"], lw=4, alpha=0.25) + for file in df['File Label'].unique() + for strand in ["+", "-"] ] -ax.legend(custom_lines, ["Total +", "Total -", "PolyA +", "PolyA -"], title="File : Strand") +ax.legend( + custom_lines, + [f"{file} : {strand}" for file in df['File Label'].unique() for strand in ["+", "-"]], + title="File : Strand" +) plt.title('Start Locations of circRNA by Chromosome and Strand') + plot_file_name = f"{input_bed_file_1.replace('.bed','')}_{input_bed_file_2.replace('.bed','')}_mqc.png" + # Save the plot plt.savefig(plot_file_name, bbox_inches='tight') diff --git a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py index 4a69874a..b77c98c4 100644 --- a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py +++ b/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py @@ -55,8 +55,8 @@ def calculate_correlation(bed_file_path, depth_file_path): for path in paths: path = path.strip() basename = os.path.splitext(os.path.basename(path))[0] - - if basename == id: + + if basename == id: # Calculate correlation using the provided bed and depth files corr = calculate_correlation(bed, path) # Write the correlation to stats.txt diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index 3f25857d..fc0e5dec 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -65,9 +65,8 @@ workflow BENCHMARKING { ch_seqdepths = ch_genomecov.genomecov .map { genomecov_result -> genomecov_result[1].toString() } .collectFile(name: 'genomecov_paths.txt', - newLine: true) - + ch_corr = SEQ_DEPTH_CORRELLATION(ch_real_bed, ch_seqdepths.collect()) ch_pearson = ch_corr.splitCsv(header: true, sep: "\t") From b7cbd04aad4e5ee0f784116fc1b28987eebd1321 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Thu, 11 Jul 2024 13:18:06 +0200 Subject: [PATCH 19/32] cosmetic cleanup of the benchmarking module. --- .../local/benchmarking/location_plots/main.nf | 2 ++ .../location_plots/templates/create_plots.py | 16 ++++++---------- modules/local/benchmarking/overlap_plot/main.nf | 2 ++ .../overlap_plot/templates/create_plots.py | 9 ++------- .../benchmarking/png_json/templates/json.py | 5 ----- .../local/benchmarking/seq_depth_plot/main.nf | 2 +- .../{create_plots.py => correlation.py} | 2 +- subworkflows/local/benchmarking.nf | 11 ++++++++--- 8 files changed, 22 insertions(+), 27 deletions(-) rename modules/local/benchmarking/seq_depth_plot/templates/{create_plots.py => correlation.py} (96%) diff --git a/modules/local/benchmarking/location_plots/main.nf b/modules/local/benchmarking/location_plots/main.nf index fff9da68..23784252 100644 --- a/modules/local/benchmarking/location_plots/main.nf +++ b/modules/local/benchmarking/location_plots/main.nf @@ -6,8 +6,10 @@ process LOCATION_PLOT { input: tuple val(id), path(bedfile1), path(bedfile2) + output: path("*_mqc.png") + script: template "create_plots.py" } diff --git a/modules/local/benchmarking/location_plots/templates/create_plots.py b/modules/local/benchmarking/location_plots/templates/create_plots.py index 32e63180..311f1aaa 100755 --- a/modules/local/benchmarking/location_plots/templates/create_plots.py +++ b/modules/local/benchmarking/location_plots/templates/create_plots.py @@ -1,16 +1,14 @@ #!/usr/bin/env python3 import csv -import os import matplotlib.pyplot as plt import seaborn as sns import pandas as pd from matplotlib.lines import Line2D -# Inputs directly from Nextflow variables input_bed_file_1 = '$bedfile1' input_bed_file_2 = '$bedfile2' -# Read input files function +# Read input files def read_bed_file(file_path, label): data = {'chromosome': [], 'start': [], 'strand': [], 'file_label': []} with open(file_path, 'r') as file: @@ -18,11 +16,10 @@ def read_bed_file(file_path, label): for row in reader: data['chromosome'].append(row[0]) data['start'].append(int(row[1])) - data['strand'].append(row[3]) # Assuming strand information is in the 4th column - data['file_label'].append(label.lower()) # Label to indicate the source file + data['strand'].append(row[3]) + data['file_label'].append(label.lower()) return data -# Combine data function def combine_data(data1, data2): for key in data1: data1[key].extend(data2[key]) @@ -45,10 +42,9 @@ def combine_data(data1, data2): # Sort DataFrame to ensure consistent plotting order df.sort_values(by=['File Label', 'Strand'], inplace=True) -# Create figure and axes +# Plotting fig, ax = plt.subplots(figsize=(12, 6)) -# Define the color palette palette = { "total +": "red", "total -": "lightcoral", @@ -56,7 +52,7 @@ def combine_data(data1, data2): "polya -": "lightblue" } -# Draw violins for each file separately +# Draw violins for file_label in df['File Label'].unique(): sns.violinplot( x="Chromosome", @@ -76,7 +72,7 @@ def combine_data(data1, data2): for violin in ax.collections: violin.set_alpha(0.25) -# Compose a custom legend +# Legend custom_lines = [ Line2D([0], [0], color=palette[f"{file} {strand}"], lw=4, alpha=0.25) for file in df['File Label'].unique() diff --git a/modules/local/benchmarking/overlap_plot/main.nf b/modules/local/benchmarking/overlap_plot/main.nf index b016b53b..4970287e 100644 --- a/modules/local/benchmarking/overlap_plot/main.nf +++ b/modules/local/benchmarking/overlap_plot/main.nf @@ -7,8 +7,10 @@ process OVERLAP_PLOT { input: tuple val(meta), path(bed) path "versions.yml" + output: path("*_mqc.png") , emit: report + script: template "create_plots.py" } diff --git a/modules/local/benchmarking/overlap_plot/templates/create_plots.py b/modules/local/benchmarking/overlap_plot/templates/create_plots.py index 892a788b..38230013 100644 --- a/modules/local/benchmarking/overlap_plot/templates/create_plots.py +++ b/modules/local/benchmarking/overlap_plot/templates/create_plots.py @@ -1,14 +1,12 @@ #!/usr/bin/env python3 import csv -import os import matplotlib.pyplot as plt import seaborn as sns import pandas as pd -# Input directly from Nextflow variable input_bed_file = '$bed' -# Read input file function +# Read input file def read_bed_file(file_path): data = {'chromosome': [], 'start': [], 'strand': []} with open(file_path, 'r') as file: @@ -22,7 +20,7 @@ def read_bed_file(file_path): # Read the data data = read_bed_file(input_bed_file) -# Create a DataFrame for seaborn +# Create a DataFrame df = pd.DataFrame({ 'Chromosome': data['chromosome'], 'Start Location': data['start'], @@ -36,7 +34,4 @@ def read_bed_file(file_path): plt.legend(title="Strand") plot_file_name = f"{input_bed_file.replace('.bed','')}_overlaps_mqc.png" -# Save the plot plt.savefig(plot_file_name, bbox_inches='tight') -print("Plot saved as:", plot_file_name) -print("Current working directory:", os.getcwd()) diff --git a/modules/local/benchmarking/png_json/templates/json.py b/modules/local/benchmarking/png_json/templates/json.py index 1f16f43b..d26e7a95 100644 --- a/modules/local/benchmarking/png_json/templates/json.py +++ b/modules/local/benchmarking/png_json/templates/json.py @@ -1,20 +1,15 @@ #!/usr/bin/env python3 - import json import os import base64 -# Assuming these variables are set properly in your environment or script png = "$png" title = "$title" description = "$description" -# Ensure the png path is an absolute path absolute_path = os.path.abspath(png) - filename = os.path.basename(absolute_path) name = filename.rstrip("_mcq.png") - id = title.lower().replace(" ", "_") # Convert the PNG file to a base64 string diff --git a/modules/local/benchmarking/seq_depth_plot/main.nf b/modules/local/benchmarking/seq_depth_plot/main.nf index f147a1a7..b25312fa 100644 --- a/modules/local/benchmarking/seq_depth_plot/main.nf +++ b/modules/local/benchmarking/seq_depth_plot/main.nf @@ -11,5 +11,5 @@ process SEQ_DEPTH_CORRELLATION { output: path("*.tsv") , emit: report script: - template "create_plots.py" + template "correlation.py" } diff --git a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py b/modules/local/benchmarking/seq_depth_plot/templates/correlation.py similarity index 96% rename from modules/local/benchmarking/seq_depth_plot/templates/create_plots.py rename to modules/local/benchmarking/seq_depth_plot/templates/correlation.py index b77c98c4..f2afe6ff 100644 --- a/modules/local/benchmarking/seq_depth_plot/templates/create_plots.py +++ b/modules/local/benchmarking/seq_depth_plot/templates/correlation.py @@ -57,7 +57,7 @@ def calculate_correlation(bed_file_path, depth_file_path): basename = os.path.splitext(os.path.basename(path))[0] if basename == id: - # Calculate correlation using the provided bed and depth files + # Calculate correlation corr = calculate_correlation(bed, path) # Write the correlation to stats.txt with open('corr_mqc.tsv', 'w') as outfile: diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index fc0e5dec..edd848f9 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -24,7 +24,8 @@ workflow BENCHMARKING { ch_trim_report main: - + + //data preparation ch_versions = Channel.empty() ch_all = ch_real_bed.mix(ch_benchmarking_bed) @@ -44,14 +45,17 @@ workflow BENCHMARKING { ch_joined = ch_merged.real.map{ meta, bed -> [[id: meta.tool], bed]} .join(ch_merged.benchmarking.map{ meta, bed -> [[id: meta.tool], bed]}) + //Overlap plot ch_intersect = BEDTOOLS_INTERSECT(ch_joined,[[], []]) - OVERLAP_PLOT(ch_intersect) OVERLAP_JSON(OVERLAP_PLOT.out, "Overlap plots", "Plot the overlap circRNAs found in total and polyA data for the tools") + //Location plot workflow LOCATION_PLOT(ch_joined) LOCATION_JSON(LOCATION_PLOT.out, "Location plots", "Plots the location of the circRNAs found" ) + + //Pearson correllation workflow ch_meta = ch_real_bam.map { it[0] } ch_path = ch_real_bam.map { it[1] } ch_scale = Channel.value(1) @@ -80,7 +84,7 @@ workflow BENCHMARKING { AVERGAGE_TSV(ch_pearson) CORRELATION_MULTIQC(AVERGAGE_TSV.out) - + //Jaccard Workflow ch_jaccard = BEDTOOLS_JACCARD(ch_joined, [[], []]).tsv ch_stats = ch_jaccard.splitCsv(header: true, sep: "\t") @@ -93,6 +97,7 @@ workflow BENCHMARKING { JACCARD_MULTIQC(ch_stats) + //combine results ch_versions = ch_versions.mix(SORT.out.versions) ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) ch_versions = ch_versions.mix(BEDTOOLS_JACCARD.out.versions) From 3039a80244cd89cf9583ceb69f415a538768564a Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Thu, 11 Jul 2024 13:54:36 +0200 Subject: [PATCH 20/32] Fixed an issue where CIRCRNA_DISCOVERY_BENCHMARKING did not get all necessary inputs after the merge --- subworkflows/local/benchmarking.nf | 2 +- workflows/circrna/main.nf | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index edd848f9..053fb9a6 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -24,7 +24,7 @@ workflow BENCHMARKING { ch_trim_report main: - + //data preparation ch_versions = Channel.empty() diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 44e9a565..f1e07506 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -176,6 +176,7 @@ workflow CIRCRNA { chromosomes, hisat2_index, star_index, + ch_annotation, params.bsj_reads, params.tool_filter, params.duplicates_fun, From 426595049b8c8c82c8dbd9f22ee8eb6cc98f5e23 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Thu, 18 Jul 2024 14:45:17 +0200 Subject: [PATCH 21/32] readded missing module configs after rebase --- conf/modules.config | 13 +++++++++++++ subworkflows/local/benchmarking.nf | 1 + subworkflows/local/circrna_discovery.nf | 2 +- 3 files changed, 15 insertions(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index e6fd3789..3b7950e3 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -629,6 +629,19 @@ process { ext.suffix = "_benchmarking.tidy.bed" } + withName: '.*:BENCHMARKING:SORT' { + ext.args = "-k 1,1 -k2,2n -k3,3n -u" + ext.suffix = "combined.bed" + } + + withName: '.*:BENCHMARKING:BEDTOOLS_MERGE' { + ext.args = "-s -c 6 -o distinct" + } + + withName: '.*:BENCHMARKING:BEDTOOLS_GENOMECOV' { + ext.args = "-dz" + } + withName: COMBINE_TRANSCRIPTOME_GTFS { ext.args = "-k 1,1 -k4,4n -k5,5n" ext.suffix = "gtf" diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index 053fb9a6..a1de025a 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -34,6 +34,7 @@ workflow BENCHMARKING { benchmarking: meta.benchmarking], bed]} .groupTuple() + ch_all.view {"all: $it"} SORT(ch_all) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 5f3c2513..46e5b1fc 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -158,7 +158,7 @@ workflow CIRCRNA_DISCOVERY { emit: - tool_bed = ANNOTATION.out.merged_bed + circrna_bed12 = ANNOTATION.out.merged_bed fasta = ADD_BACKSPLICE.out.output annotation_bed = ANNOTATION.out.bed annotation_gtf = ANNOTATION.out.gtf From 1fefca719bc6f24c3ac829cd7b542d42363a6ebd Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Thu, 1 Aug 2024 11:46:38 +0200 Subject: [PATCH 22/32] Ensured correct syntax, removed unnecessary specifications --- modules/local/benchmarking/average_tsv/templates/average.py | 4 ++-- modules/local/benchmarking/location_plots/main.nf | 2 +- .../benchmarking/location_plots/templates/create_plots.py | 2 +- modules/local/benchmarking/overlap_plot/main.nf | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/local/benchmarking/average_tsv/templates/average.py b/modules/local/benchmarking/average_tsv/templates/average.py index b749366d..d1ee3e15 100644 --- a/modules/local/benchmarking/average_tsv/templates/average.py +++ b/modules/local/benchmarking/average_tsv/templates/average.py @@ -3,11 +3,11 @@ import pandas as pd tsv = "$tsv" -data = pd.read_csv(tsv, sep='\t') +data = pd.read_csv(tsv, sep='\\t') data['tool'] = data['tool'].str.replace('tool:', '') average_values = data.groupby('tool')['pearson_corr'].mean().reset_index() output_file_path = tsv -average_values.to_csv(output_file_path, sep='\t', index=False) +average_values.to_csv(output_file_path, sep='\\t', index=False) diff --git a/modules/local/benchmarking/location_plots/main.nf b/modules/local/benchmarking/location_plots/main.nf index 23784252..28a5fa73 100644 --- a/modules/local/benchmarking/location_plots/main.nf +++ b/modules/local/benchmarking/location_plots/main.nf @@ -1,7 +1,7 @@ process LOCATION_PLOT { label "process_single" - conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2" + conda "bioconda::seaborn=0.11.2" container 'uphl/seaborn' input: diff --git a/modules/local/benchmarking/location_plots/templates/create_plots.py b/modules/local/benchmarking/location_plots/templates/create_plots.py index 311f1aaa..f99d4e42 100755 --- a/modules/local/benchmarking/location_plots/templates/create_plots.py +++ b/modules/local/benchmarking/location_plots/templates/create_plots.py @@ -12,7 +12,7 @@ def read_bed_file(file_path, label): data = {'chromosome': [], 'start': [], 'strand': [], 'file_label': []} with open(file_path, 'r') as file: - reader = csv.reader(file, delimiter='\t') + reader = csv.reader(file, delimiter='\\t') for row in reader: data['chromosome'].append(row[0]) data['start'].append(int(row[1])) diff --git a/modules/local/benchmarking/overlap_plot/main.nf b/modules/local/benchmarking/overlap_plot/main.nf index 4970287e..bf2b6c0f 100644 --- a/modules/local/benchmarking/overlap_plot/main.nf +++ b/modules/local/benchmarking/overlap_plot/main.nf @@ -1,7 +1,7 @@ process OVERLAP_PLOT { label "process_single" - conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2" + conda "bioconda::seaborn=0.11.2" container 'uphl/seaborn' input: From 74a243abf676ac28ba2a85e22183fcd88f09f62f Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Thu, 1 Aug 2024 12:31:27 +0200 Subject: [PATCH 23/32] removed debugging statements --- conf/modules.config | 4 ++-- subworkflows/local/benchmarking.nf | 2 -- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 5aead744..fc89e216 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -342,8 +342,8 @@ process { } withName: '.*:FIND_CIRC:UNIFY' { - // Keep only rows with UNAMBIGUOUS_BP and ANCHOR_UNIQUE in $18 - ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$18 ~ /UNAMBIGUOUS_BP/ && \$18 ~ /ANCHOR_UNIQUE/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" + // Keep only rows with CIRCULAR, UNAMBIGUOUS_BP and ANCHOR_UNIQUE in $18 + ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$18 ~ /CIRCULAR/ && \$18 ~ /UNAMBIGUOUS_BP/ && \$18 ~ /ANCHOR_UNIQUE/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" ext.suffix = "find_circ.bed" publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/${meta.id}" }, diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index a1de025a..660ca896 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -34,8 +34,6 @@ workflow BENCHMARKING { benchmarking: meta.benchmarking], bed]} .groupTuple() - ch_all.view {"all: $it"} - SORT(ch_all) BEDTOOLS_MERGE(SORT.out.sorted).bed.branch{ meta, bed -> From 78e8c1183be3fd988a609cfbb909a10712802b12 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Mon, 19 Aug 2024 15:07:55 +0200 Subject: [PATCH 24/32] added version control as per requested changes (15.07.24) and GENOMECOV --- .../local/benchmarking/average_tsv/main.nf | 5 +-- .../average_tsv/templates/average.py | 30 +++++++++++++++++ .../local/benchmarking/location_plots/main.nf | 3 +- .../location_plots/templates/create_plots.py | 31 ++++++++++++++++++ .../local/benchmarking/overlap_plot/main.nf | 3 +- .../overlap_plot/templates/create_plots.py | 32 +++++++++++++++++++ modules/local/benchmarking/png_json/main.nf | 1 + .../benchmarking/png_json/templates/json.py | 28 ++++++++++++++++ .../local/benchmarking/seq_depth_plot/main.nf | 1 + .../seq_depth_plot/templates/correlation.py | 30 +++++++++++++++++ subworkflows/local/benchmarking.nf | 21 ++++++++---- 11 files changed, 175 insertions(+), 10 deletions(-) diff --git a/modules/local/benchmarking/average_tsv/main.nf b/modules/local/benchmarking/average_tsv/main.nf index fe4cac93..79a0b5c1 100644 --- a/modules/local/benchmarking/average_tsv/main.nf +++ b/modules/local/benchmarking/average_tsv/main.nf @@ -1,4 +1,4 @@ -process AVERGAGE_TSV { +process AVERAGE_TSV { label "process_single" conda "bioconda::pandas=1.5.2" @@ -11,7 +11,8 @@ process AVERGAGE_TSV { path(tsv) output: - path(tsv) + path(tsv), emit: tsv + path("versions.yml"), emit: versions script: template "average.py" diff --git a/modules/local/benchmarking/average_tsv/templates/average.py b/modules/local/benchmarking/average_tsv/templates/average.py index d1ee3e15..54f27a37 100644 --- a/modules/local/benchmarking/average_tsv/templates/average.py +++ b/modules/local/benchmarking/average_tsv/templates/average.py @@ -1,6 +1,7 @@ #!/usr/bin/env python3 import pandas as pd +import platform tsv = "$tsv" data = pd.read_csv(tsv, sep='\\t') @@ -11,3 +12,32 @@ output_file_path = tsv average_values.to_csv(output_file_path, sep='\\t', index=False) +#version capture +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. + + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str + +versions = { + "${task.process}" : { + "python": platform.python_version(), + "pandas": pd.__version__ + } +} +with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) + diff --git a/modules/local/benchmarking/location_plots/main.nf b/modules/local/benchmarking/location_plots/main.nf index 28a5fa73..e044f18a 100644 --- a/modules/local/benchmarking/location_plots/main.nf +++ b/modules/local/benchmarking/location_plots/main.nf @@ -8,7 +8,8 @@ process LOCATION_PLOT { tuple val(id), path(bedfile1), path(bedfile2) output: - path("*_mqc.png") + path("*_mqc.png"), emit: plots + path("versions.yml"), emit: versions script: template "create_plots.py" diff --git a/modules/local/benchmarking/location_plots/templates/create_plots.py b/modules/local/benchmarking/location_plots/templates/create_plots.py index f99d4e42..1479bc84 100755 --- a/modules/local/benchmarking/location_plots/templates/create_plots.py +++ b/modules/local/benchmarking/location_plots/templates/create_plots.py @@ -4,6 +4,7 @@ import seaborn as sns import pandas as pd from matplotlib.lines import Line2D +import platform input_bed_file_1 = '$bedfile1' input_bed_file_2 = '$bedfile2' @@ -90,3 +91,33 @@ def combine_data(data1, data2): # Save the plot plt.savefig(plot_file_name, bbox_inches='tight') + +#version capture +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. + + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str + +versions = { + "${task.process}" : { + "python": platform.python_version(), + "pandas": pd.__version__, + "seaborn": sns.__version__ + } +} +with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) diff --git a/modules/local/benchmarking/overlap_plot/main.nf b/modules/local/benchmarking/overlap_plot/main.nf index bf2b6c0f..0e94756a 100644 --- a/modules/local/benchmarking/overlap_plot/main.nf +++ b/modules/local/benchmarking/overlap_plot/main.nf @@ -9,7 +9,8 @@ process OVERLAP_PLOT { path "versions.yml" output: - path("*_mqc.png") , emit: report + path("*_mqc.png") , emit: plots + path("versions.yml"), emit: versions script: template "create_plots.py" diff --git a/modules/local/benchmarking/overlap_plot/templates/create_plots.py b/modules/local/benchmarking/overlap_plot/templates/create_plots.py index 38230013..fcbae5ea 100644 --- a/modules/local/benchmarking/overlap_plot/templates/create_plots.py +++ b/modules/local/benchmarking/overlap_plot/templates/create_plots.py @@ -3,6 +3,7 @@ import matplotlib.pyplot as plt import seaborn as sns import pandas as pd +import platform input_bed_file = '$bed' @@ -35,3 +36,34 @@ def read_bed_file(file_path): plot_file_name = f"{input_bed_file.replace('.bed','')}_overlaps_mqc.png" plt.savefig(plot_file_name, bbox_inches='tight') + + +#version capture +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. + + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str + +versions = { + "${task.process}" : { + "python": platform.python_version(), + "pandas": pd.__version__, + "seaborn": sns.__version__ + } +} +with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) diff --git a/modules/local/benchmarking/png_json/main.nf b/modules/local/benchmarking/png_json/main.nf index fab4be69..e6205bfc 100644 --- a/modules/local/benchmarking/png_json/main.nf +++ b/modules/local/benchmarking/png_json/main.nf @@ -13,6 +13,7 @@ process PNG_JSON { output: path("*_mqc.json") , emit: report + path("versions.yml"), emit: versions script: template "json.py" diff --git a/modules/local/benchmarking/png_json/templates/json.py b/modules/local/benchmarking/png_json/templates/json.py index d26e7a95..639cfab2 100644 --- a/modules/local/benchmarking/png_json/templates/json.py +++ b/modules/local/benchmarking/png_json/templates/json.py @@ -2,6 +2,7 @@ import json import os import base64 +import platform png = "$png" title = "$title" @@ -33,3 +34,30 @@ print(f"JSON file created for {absolute_path}") +#version capture +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. + + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str + +versions = { + "${task.process}" : { + "python": platform.python_version() + } +} +with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) diff --git a/modules/local/benchmarking/seq_depth_plot/main.nf b/modules/local/benchmarking/seq_depth_plot/main.nf index b25312fa..9a36215d 100644 --- a/modules/local/benchmarking/seq_depth_plot/main.nf +++ b/modules/local/benchmarking/seq_depth_plot/main.nf @@ -10,6 +10,7 @@ process SEQ_DEPTH_CORRELLATION { path(depth) output: path("*.tsv") , emit: report + path("versions.yml"), emit: versions script: template "correlation.py" } diff --git a/modules/local/benchmarking/seq_depth_plot/templates/correlation.py b/modules/local/benchmarking/seq_depth_plot/templates/correlation.py index f2afe6ff..326256aa 100644 --- a/modules/local/benchmarking/seq_depth_plot/templates/correlation.py +++ b/modules/local/benchmarking/seq_depth_plot/templates/correlation.py @@ -1,6 +1,7 @@ #!/usr/bin/env python3 import os import re +import platform import numpy as np meta = "$meta" @@ -63,3 +64,32 @@ def calculate_correlation(bed_file_path, depth_file_path): with open('corr_mqc.tsv', 'w') as outfile: header = "tool\\tpearson_corr\\n" outfile.write(header + meta.split(",")[4][:-1] + '\\t' + str(corr)) + +#version capture +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. + + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str + +versions = { + "${task.process}" : { + "python": platform.python_version(), + "numpy": np.__version__ + } +} +with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index 660ca896..97aba82f 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -10,7 +10,7 @@ include { PNG_JSON as OVERLAP_JSON } from '../../modules/local/benchmarking/png include { LOCATION_PLOT } from '../../modules/local/benchmarking/location_plots' include { OVERLAP_PLOT } from '../../modules/local/benchmarking/overlap_plot' include { SEQ_DEPTH_CORRELLATION } from '../../modules/local/benchmarking/seq_depth_plot' -include { AVERGAGE_TSV } from '../../modules/local/benchmarking/average_tsv' +include { AVERAGE_TSV } from '../../modules/local/benchmarking/average_tsv' @@ -47,11 +47,11 @@ workflow BENCHMARKING { //Overlap plot ch_intersect = BEDTOOLS_INTERSECT(ch_joined,[[], []]) OVERLAP_PLOT(ch_intersect) - OVERLAP_JSON(OVERLAP_PLOT.out, "Overlap plots", "Plot the overlap circRNAs found in total and polyA data for the tools") + OVERLAP_JSON(OVERLAP_PLOT.out.plots, "Overlap plots", "Plot the overlap circRNAs found in total and polyA data for the tools") //Location plot workflow LOCATION_PLOT(ch_joined) - LOCATION_JSON(LOCATION_PLOT.out, "Location plots", "Plots the location of the circRNAs found" ) + LOCATION_JSON(LOCATION_PLOT.out.plots, "Location plots", "Plots the location of the circRNAs found" ) //Pearson correllation workflow @@ -70,7 +70,7 @@ workflow BENCHMARKING { .collectFile(name: 'genomecov_paths.txt', newLine: true) - ch_corr = SEQ_DEPTH_CORRELLATION(ch_real_bed, ch_seqdepths.collect()) + ch_corr = SEQ_DEPTH_CORRELLATION(ch_real_bed, ch_seqdepths.collect()).report ch_pearson = ch_corr.splitCsv(header: true, sep: "\t") .map{ values -> [values.tool, values.pearson_corr]} @@ -80,8 +80,8 @@ workflow BENCHMARKING { row -> ["pearson.tsv", row.join("\t")] } - AVERGAGE_TSV(ch_pearson) - CORRELATION_MULTIQC(AVERGAGE_TSV.out) + AVERAGE_TSV(ch_pearson) + CORRELATION_MULTIQC(AVERAGE_TSV.out.tsv) //Jaccard Workflow ch_jaccard = BEDTOOLS_JACCARD(ch_joined, [[], []]).tsv @@ -100,7 +100,16 @@ workflow BENCHMARKING { ch_versions = ch_versions.mix(SORT.out.versions) ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) ch_versions = ch_versions.mix(BEDTOOLS_JACCARD.out.versions) + ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions) + ch_versions = ch_versions.mix(BEDTOOLS_INTERSECT.out.versions) ch_versions = ch_versions.mix(JACCARD_MULTIQC.out.versions) + ch_versions = ch_versions.mix(AVERAGE_TSV.out.versions) + ch_versions = ch_versions.mix(OVERLAP_PLOT.out.versions) + ch_versions = ch_versions.mix(OVERLAP_JSON.out.versions) + ch_versions = ch_versions.mix(LOCATION_PLOT.out.versions) + ch_versions = ch_versions.mix(LOCATION_JSON.out.versions) + ch_versions = ch_versions.mix(SEQ_DEPTH_CORRELLATION.out.versions) + ch_versions = ch_versions.mix(CORRELATION_MULTIQC.out.versions) ch_reports = JACCARD_MULTIQC.out.report.mix(LOCATION_JSON.out.report) From f7bbcbba7ade9a36b700e8b43cc74c820ede6b35 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 5 Sep 2024 17:35:08 +0200 Subject: [PATCH 25/32] Minor adjustments for compatibility --- subworkflows/local/bsj_detection.nf | 16 +++++++++------- workflows/circrna/main.nf | 4 ++-- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/subworkflows/local/bsj_detection.nf b/subworkflows/local/bsj_detection.nf index 89ddec4e..d85bf330 100644 --- a/subworkflows/local/bsj_detection.nf +++ b/subworkflows/local/bsj_detection.nf @@ -229,11 +229,13 @@ workflow BSJ_DETECTION { ) emit: - bed = ch_bsj_bed_combined - bed12 = ch_bsj_bed12_combined - gtf = ch_bsj_gtf_combined - fasta = ch_bsj_fasta_combined - - multiqc_files = ch_multiqc_files - versions = ch_versions + bed = ch_bsj_bed_combined + bed12 = ch_bsj_bed12_combined + gtf = ch_bsj_gtf_combined + fasta = ch_bsj_fasta_combined + star_bam = STAR2PASS.out.bam + bed_per_sample_tool = ch_bsj_bed_per_sample_tool + + multiqc_files = ch_multiqc_files + versions = ch_versions } diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 540dff5b..e3ed243f 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -184,8 +184,8 @@ workflow CIRCRNA { ) BENCHMARKING( - BSJ_DETECTION.out.tool_bed, - BSJ_DETECTION_BENCHMARKING.out.tool_bed, + BSJ_DETECTION.out.bed_per_sample_tool, + BSJ_DETECTION_BENCHMARKING.out.bed_per_sample_tool, BSJ_DETECTION.out.star_bam, BSJ_DETECTION_BENCHMARKING.out.star_bam, FASTQC_TRIMGALORE.out.trim_log From c2b76e67d1ce859b14e8f0441f32d4197f976512 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 5 Sep 2024 17:39:40 +0200 Subject: [PATCH 26/32] Remove outdated module configs --- conf/modules.config | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index c149b547..765827fc 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -813,20 +813,6 @@ process { ] } - withName: COUNTS_COMBINED { - ext.when = { params.module.split(',').contains('circrna_discovery') } - } - - withName: COUNTS_TO_BED { - ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\" }'" - ext.suffix = "bed" - } - - withName: UNIQUE_REGIONS { - ext.args = "-k 1,1 -k2,2n -k3,3n -u" - ext.suffix = "unique.bed" - } - withName: '.*:CIRCRNA_DISCOVERY_BENCHMARKING:ANNOTATION:REMOVE_SCORE_STRAND' { ext.suffix = "_benchmarking.tidy.bed" } From 467e61719a25bce049f4df83cca8de527c80ce27 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 5 Sep 2024 17:41:12 +0200 Subject: [PATCH 27/32] Remove some unnecessary imports --- subworkflows/local/annotation.nf | 1 - subworkflows/local/mirna_prediction.nf | 7 +++---- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/annotation.nf b/subworkflows/local/annotation.nf index dea819a6..e14290c5 100644 --- a/subworkflows/local/annotation.nf +++ b/subworkflows/local/annotation.nf @@ -1,6 +1,5 @@ include { BEDTOOLS_INTERSECT as INTERSECT_GTF } from '../../modules/nf-core/bedtools/intersect' include { GAWK as INGEST_DATABASE_NAMES } from '../../modules/nf-core/gawk' -include { GNU_SORT as COMBINE_DATABASES } from '../../modules/nf-core/gnu/sort' include { BEDTOOLS_INTERSECT as INTERSECT_DATABASE } from '../../modules/nf-core/bedtools/intersect' include { ANNOTATION as ANNOTATE } from '../../modules/local/annotation' diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index b3fc46cc..1b6b046b 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -1,8 +1,7 @@ // MODULES -include { BIOAWK as ADD_BACKSPLICE } from '../../modules/nf-core/bioawk' -include { DESEQ2_NORMALIZATION } from '../../modules/local/deseq2/normalization' -include { MIRNA_FILTERING } from '../../modules/local/mirna_filtering' -include { COMPUTE_CORRELATIONS } from '../../modules/local/compute_correlations' +include { DESEQ2_NORMALIZATION } from '../../modules/local/deseq2/normalization' +include { MIRNA_FILTERING } from '../../modules/local/mirna_filtering' +include { COMPUTE_CORRELATIONS } from '../../modules/local/compute_correlations' // SUBWORKFLOWS include { MIRNA_BINDINGSITES } from './mirna/mirna_bindingsites' From a06a53a19e8c1eb04b158b508ff5fd5dde560ed1 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Fri, 13 Sep 2024 12:44:26 +0200 Subject: [PATCH 28/32] implemented requested changes from 5.9.24 --- .../local/benchmarking/location_plots/main.nf | 5 ++- modules/local/benchmarking/multiqc/main.nf | 1 + .../local/benchmarking/overlap_plot/main.nf | 4 +- modules/local/benchmarking/png_json/main.nf | 1 + .../local/benchmarking/seq_depth_plot/main.nf | 1 + nextflow_schema.json | 2 +- subworkflows/local/benchmarking.nf | 41 ++++++++++++------- workflows/circrna/main.nf | 4 +- 8 files changed, 36 insertions(+), 23 deletions(-) diff --git a/modules/local/benchmarking/location_plots/main.nf b/modules/local/benchmarking/location_plots/main.nf index e044f18a..4b4747bf 100644 --- a/modules/local/benchmarking/location_plots/main.nf +++ b/modules/local/benchmarking/location_plots/main.nf @@ -1,11 +1,12 @@ process LOCATION_PLOT { + tag "$meta.id" label "process_single" conda "bioconda::seaborn=0.11.2" - container 'uphl/seaborn' + container 'community.wave.seqera.io/library/seaborn:0.13.2--ef0811a05c6fcc75' input: - tuple val(id), path(bedfile1), path(bedfile2) + tuple val(meta), path(bedfile1), path(bedfile2) output: path("*_mqc.png"), emit: plots diff --git a/modules/local/benchmarking/multiqc/main.nf b/modules/local/benchmarking/multiqc/main.nf index a39675d3..0119e418 100644 --- a/modules/local/benchmarking/multiqc/main.nf +++ b/modules/local/benchmarking/multiqc/main.nf @@ -1,4 +1,5 @@ process BENCHMARKING_MULTIQC { + tag "$meta.id" label "process_single" conda "bioconda::pandas=1.5.2" diff --git a/modules/local/benchmarking/overlap_plot/main.nf b/modules/local/benchmarking/overlap_plot/main.nf index 0e94756a..161b6203 100644 --- a/modules/local/benchmarking/overlap_plot/main.nf +++ b/modules/local/benchmarking/overlap_plot/main.nf @@ -1,12 +1,12 @@ process OVERLAP_PLOT { + tag "$meta.id" label "process_single" conda "bioconda::seaborn=0.11.2" - container 'uphl/seaborn' + container 'community.wave.seqera.io/library/seaborn:0.13.2--ef0811a05c6fcc75' input: tuple val(meta), path(bed) - path "versions.yml" output: path("*_mqc.png") , emit: plots diff --git a/modules/local/benchmarking/png_json/main.nf b/modules/local/benchmarking/png_json/main.nf index e6205bfc..b2618ddc 100644 --- a/modules/local/benchmarking/png_json/main.nf +++ b/modules/local/benchmarking/png_json/main.nf @@ -1,4 +1,5 @@ process PNG_JSON { + tag "$meta.id" label "process_single" conda "bioconda::pandas=1.5.2" diff --git a/modules/local/benchmarking/seq_depth_plot/main.nf b/modules/local/benchmarking/seq_depth_plot/main.nf index 9a36215d..cdb5c1ed 100644 --- a/modules/local/benchmarking/seq_depth_plot/main.nf +++ b/modules/local/benchmarking/seq_depth_plot/main.nf @@ -1,4 +1,5 @@ process SEQ_DEPTH_CORRELLATION { + tag "$meta.id" label "process_single" conda "bioconda::matplotlib=3.5.1 bioconda::seaborn=0.11.2" diff --git a/nextflow_schema.json b/nextflow_schema.json index a8b1fe86..268428f7 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -144,7 +144,7 @@ "description": "Run the pipeline in benchmarking mode.", "default": false, "fa_icon": "fas fa-chart-line", - "help_text": "This enables parallel analysis of polyA-enriched data with the same circRNA quantification tools to compare performance." + "help_text": "This enables parallel analysis of polyA-enriched data with the same circRNA quantification tools to compare results." }, "mirna_tools": { "type": "string", diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index 97aba82f..3197d7af 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -35,24 +35,30 @@ workflow BENCHMARKING { .groupTuple() SORT(ch_all) + ch_versions = ch_versions.mix(SORT.out.versions) BEDTOOLS_MERGE(SORT.out.sorted).bed.branch{ meta, bed -> real: !meta.benchmarking benchmarking: meta.benchmarking }.set { ch_merged } + ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) ch_joined = ch_merged.real.map{ meta, bed -> [[id: meta.tool], bed]} .join(ch_merged.benchmarking.map{ meta, bed -> [[id: meta.tool], bed]}) //Overlap plot ch_intersect = BEDTOOLS_INTERSECT(ch_joined,[[], []]) - OVERLAP_PLOT(ch_intersect) + OVERLAP_PLOT(ch_intersect.out.intersect) OVERLAP_JSON(OVERLAP_PLOT.out.plots, "Overlap plots", "Plot the overlap circRNAs found in total and polyA data for the tools") + ch_versions = ch_versions.mix(BEDTOOLS_INTERSECT.out.versions) + ch_versions = ch_versions.mix(OVERLAP_PLOT.out.versions) + ch_versions = ch_versions.mix(OVERLAP_JSON.out.versions) //Location plot workflow LOCATION_PLOT(ch_joined) LOCATION_JSON(LOCATION_PLOT.out.plots, "Location plots", "Plots the location of the circRNAs found" ) - + ch_versions = ch_versions.mix(LOCATION_PLOT.out.versions) + ch_versions = ch_versions.mix(LOCATION_JSON.out.versions) //Pearson correllation workflow ch_meta = ch_real_bam.map { it[0] } @@ -64,6 +70,7 @@ workflow BENCHMARKING { } ch_genomecov = BEDTOOLS_GENOMECOV(ch_genomecov_inputs, [], "bg",false) + ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions) ch_seqdepths = ch_genomecov.genomecov .map { genomecov_result -> genomecov_result[1].toString() } @@ -71,6 +78,7 @@ workflow BENCHMARKING { newLine: true) ch_corr = SEQ_DEPTH_CORRELLATION(ch_real_bed, ch_seqdepths.collect()).report + ch_versions = ch_versions.mix(SEQ_DEPTH_CORRELLATION.out.versions) ch_pearson = ch_corr.splitCsv(header: true, sep: "\t") .map{ values -> [values.tool, values.pearson_corr]} @@ -82,9 +90,12 @@ workflow BENCHMARKING { AVERAGE_TSV(ch_pearson) CORRELATION_MULTIQC(AVERAGE_TSV.out.tsv) + ch_versions = ch_versions.mix(AVERAGE_TSV.out.versions) + ch_versions = ch_versions.mix(CORRELATION_MULTIQC.out.versions) //Jaccard Workflow ch_jaccard = BEDTOOLS_JACCARD(ch_joined, [[], []]).tsv + ch_versions = ch_versions.mix(BEDTOOLS_JACCARD.out.versions) ch_stats = ch_jaccard.splitCsv(header: true, sep: "\t") .map{ meta, values -> [meta.id, values.intersection, values.union, values.jaccard, values.n_intersections]} @@ -95,22 +106,22 @@ workflow BENCHMARKING { } JACCARD_MULTIQC(ch_stats) + ch_versions = ch_versions.mix(JACCARD_MULTIQC.out.versions) //combine results - ch_versions = ch_versions.mix(SORT.out.versions) - ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) - ch_versions = ch_versions.mix(BEDTOOLS_JACCARD.out.versions) - ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions) - ch_versions = ch_versions.mix(BEDTOOLS_INTERSECT.out.versions) - ch_versions = ch_versions.mix(JACCARD_MULTIQC.out.versions) - ch_versions = ch_versions.mix(AVERAGE_TSV.out.versions) - ch_versions = ch_versions.mix(OVERLAP_PLOT.out.versions) - ch_versions = ch_versions.mix(OVERLAP_JSON.out.versions) - ch_versions = ch_versions.mix(LOCATION_PLOT.out.versions) - ch_versions = ch_versions.mix(LOCATION_JSON.out.versions) - ch_versions = ch_versions.mix(SEQ_DEPTH_CORRELLATION.out.versions) - ch_versions = ch_versions.mix(CORRELATION_MULTIQC.out.versions) + + + + + + + + + + + + ch_reports = JACCARD_MULTIQC.out.report.mix(LOCATION_JSON.out.report) ch_reports = ch_reports.mix(OVERLAP_JSON.out.report) diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index e3ed243f..0d425991 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -170,16 +170,14 @@ workflow CIRCRNA { ch_reads.benchmarking, ch_fasta, ch_gtf, + ch_annotation, bowtie_index, bowtie2_index, bwa_index, chromosomes, hisat2_index, star_index, - ch_annotation, params.bsj_reads, - params.tool_filter, - params.duplicates_fun, params.exon_boundary ) From c4f4b3c7ce89f10467c3dc28ea4f4b1c45f40d3c Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Mon, 16 Sep 2024 12:36:13 +0200 Subject: [PATCH 29/32] fixed some issues that pervented termination --- modules/local/benchmarking/multiqc/main.nf | 1 - modules/local/benchmarking/png_json/main.nf | 1 - .../seq_depth_plot/templates/correlation.py | 1 + subworkflows/local/benchmarking.nf | 16 +--------------- workflows/circrna/main.nf | 2 +- 5 files changed, 3 insertions(+), 18 deletions(-) diff --git a/modules/local/benchmarking/multiqc/main.nf b/modules/local/benchmarking/multiqc/main.nf index 0119e418..a39675d3 100644 --- a/modules/local/benchmarking/multiqc/main.nf +++ b/modules/local/benchmarking/multiqc/main.nf @@ -1,5 +1,4 @@ process BENCHMARKING_MULTIQC { - tag "$meta.id" label "process_single" conda "bioconda::pandas=1.5.2" diff --git a/modules/local/benchmarking/png_json/main.nf b/modules/local/benchmarking/png_json/main.nf index b2618ddc..e6205bfc 100644 --- a/modules/local/benchmarking/png_json/main.nf +++ b/modules/local/benchmarking/png_json/main.nf @@ -1,5 +1,4 @@ process PNG_JSON { - tag "$meta.id" label "process_single" conda "bioconda::pandas=1.5.2" diff --git a/modules/local/benchmarking/seq_depth_plot/templates/correlation.py b/modules/local/benchmarking/seq_depth_plot/templates/correlation.py index 326256aa..78daf86d 100644 --- a/modules/local/benchmarking/seq_depth_plot/templates/correlation.py +++ b/modules/local/benchmarking/seq_depth_plot/templates/correlation.py @@ -13,6 +13,7 @@ def calculate_correlation(bed_file_path, depth_file_path): circRNA_regions = [] with open(bed_file_path, 'r') as bed_file: for line in bed_file: + if line.startswith('#'): continue parts = line.strip().split() chr = parts[0] start = int(parts[1]) diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index 3197d7af..09fbda3d 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -48,7 +48,7 @@ workflow BENCHMARKING { //Overlap plot ch_intersect = BEDTOOLS_INTERSECT(ch_joined,[[], []]) - OVERLAP_PLOT(ch_intersect.out.intersect) + OVERLAP_PLOT(ch_intersect.intersect) OVERLAP_JSON(OVERLAP_PLOT.out.plots, "Overlap plots", "Plot the overlap circRNAs found in total and polyA data for the tools") ch_versions = ch_versions.mix(BEDTOOLS_INTERSECT.out.versions) ch_versions = ch_versions.mix(OVERLAP_PLOT.out.versions) @@ -109,20 +109,6 @@ workflow BENCHMARKING { ch_versions = ch_versions.mix(JACCARD_MULTIQC.out.versions) //combine results - - - - - - - - - - - - - - ch_reports = JACCARD_MULTIQC.out.report.mix(LOCATION_JSON.out.report) ch_reports = ch_reports.mix(OVERLAP_JSON.out.report) ch_reports = ch_reports.mix(CORRELATION_MULTIQC.out.report) diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 0d425991..b656bd01 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -166,7 +166,7 @@ workflow CIRCRNA { // if (params.benchmarking) { - BSJ_DETECTION( + BSJ_DETECTION_BENCHMARKING( ch_reads.benchmarking, ch_fasta, ch_gtf, From 8f1c8f8e2501c76e65bab89a2f009d2499913bb8 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 16 Oct 2024 09:26:41 +0000 Subject: [PATCH 30/32] Template update for nf-core/tools version 3.0.2 --- .github/CONTRIBUTING.md | 12 +- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 25 +- .github/workflows/ci.yml | 57 ++- .github/workflows/download_pipeline.yml | 53 ++- .github/workflows/linting.yml | 23 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 2 +- .../workflows/template_version_comment.yml | 46 +++ .gitignore | 1 + .gitpod.yml | 7 +- .nf-core.yml | 17 +- .pre-commit-config.yaml | 2 +- CHANGELOG.md | 2 +- CITATIONS.md | 4 +- LICENSE | 2 +- README.md | 7 +- assets/schema_input.json | 2 +- conf/base.config | 34 +- conf/igenomes_ignored.config | 9 + conf/modules.config | 1 - conf/test.config | 13 +- docs/images/mqc_fastqc_adapter.png | Bin 23458 -> 0 bytes docs/images/mqc_fastqc_counts.png | Bin 33918 -> 0 bytes docs/images/mqc_fastqc_quality.png | Bin 55769 -> 0 bytes docs/output.md | 10 - docs/usage.md | 12 +- main.nf | 8 - modules.json | 12 +- modules/nf-core/fastqc/environment.yml | 2 - modules/nf-core/fastqc/main.nf | 5 +- modules/nf-core/fastqc/meta.yml | 57 +-- modules/nf-core/fastqc/tests/main.nf.test | 225 ++++++++--- .../nf-core/fastqc/tests/main.nf.test.snap | 370 ++++++++++++++++-- modules/nf-core/multiqc/environment.yml | 4 +- modules/nf-core/multiqc/main.nf | 16 +- modules/nf-core/multiqc/meta.yml | 78 ++-- modules/nf-core/multiqc/tests/main.nf.test | 8 + .../nf-core/multiqc/tests/main.nf.test.snap | 24 +- modules/nf-core/multiqc/tests/nextflow.config | 5 + nextflow.config | 148 ++++--- nextflow_schema.json | 85 +--- .../utils_nfcore_circrna_pipeline/main.nf | 66 ++-- .../nf-core/utils_nextflow_pipeline/main.nf | 70 ++-- .../tests/nextflow.config | 2 +- .../nf-core/utils_nfcore_pipeline/main.nf | 306 ++++++++------- .../nf-core/utils_nfschema_plugin/main.nf | 46 +++ .../nf-core/utils_nfschema_plugin/meta.yml | 35 ++ .../utils_nfschema_plugin/tests/main.nf.test | 117 ++++++ .../tests/nextflow.config | 8 + .../tests/nextflow_schema.json | 8 +- .../nf-core/utils_nfvalidation_plugin/main.nf | 62 --- .../utils_nfvalidation_plugin/meta.yml | 44 --- .../tests/main.nf.test | 200 ---------- .../utils_nfvalidation_plugin/tests/tags.yml | 2 - workflows/circrna.nf | 21 +- 56 files changed, 1410 insertions(+), 969 deletions(-) create mode 100644 .github/workflows/template_version_comment.yml create mode 100644 conf/igenomes_ignored.config delete mode 100755 docs/images/mqc_fastqc_adapter.png delete mode 100755 docs/images/mqc_fastqc_counts.png delete mode 100755 docs/images/mqc_fastqc_quality.png create mode 100644 modules/nf-core/multiqc/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config rename subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%) delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index d8a9ab91..ff849d6c 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/circrna, the standard workflow is a 1. Check that there isn't already an issue about your idea in the [nf-core/circrna issues](https://github.com/nf-core/circrna/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/circrna repository](https://github.com/nf-core/circrna) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). @@ -40,7 +40,7 @@ There are typically two types of tests that run: ### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. @@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards: 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. @@ -86,11 +86,11 @@ If you wish to contribute a new step, please use the following coding standards: Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. +Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. ### Default processes resource requirements -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. @@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g ### Nextflow version bumping -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` ### Images and figures diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 9d44ed38..187fef97 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/circ - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/circrna/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/circrna _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. -- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 8f7ea0eb..59013de0 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,18 +1,35 @@ name: nf-core AWS full size tests -# This workflow is triggered on published releases. +# This workflow is triggered on PRs opened against the master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: - release: - types: [published] + pull_request: + branches: + - master workflow_dispatch: + pull_request_review: + types: [submitted] + jobs: run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/circrna' + # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered + if: github.repository == 'nf-core/circrna' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest steps: + - uses: octokit/request-action@v2.x + id: check_approvals + with: + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + - id: test_variables + if: github.event_name != 'workflow_dispatch' + run: | + JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' + CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') + test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 8bfcd749..bb52ff21 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,9 +7,12 @@ on: pull_request: release: types: [published] + workflow_dispatch: env: NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" @@ -17,30 +20,66 @@ concurrency: jobs: test: - name: Run pipeline with test data + name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" # Only run on push if this is the nf-core dev branch (merged PRs) if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/circrna') }}" runs-on: ubuntu-latest strategy: matrix: NXF_VER: - - "23.04.0" + - "24.04.2" - "latest-everything" + profile: + - "conda" + - "docker" + - "singularity" + test_name: + - "test" + isMaster: + - ${{ github.base_ref == 'master' }} + # Exclude conda and singularity on dev + exclude: + - isMaster: false + profile: "conda" + - isMaster: false + profile: "singularity" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Install Nextflow + - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" - - name: Disk space cleanup + - name: Set up Apptainer + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-apptainer@main + + - name: Set up Singularity + if: matrix.profile == 'singularity' + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Set up Miniconda + if: matrix.profile == 'conda' + uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 + with: + miniconda-version: "latest" + auto-update-conda: true + conda-solver: libmamba + channels: conda-forge,bioconda + + - name: Set up Conda + if: matrix.profile == 'conda' + run: | + echo $(realpath $CONDA)/condabin >> $GITHUB_PATH + echo $(realpath python) >> $GITHUB_PATH + + - name: Clean up Disk space uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data - # TODO nf-core: You can customise CI pipeline run tests as required - # For example: adding multiple test runs with different parameters - # Remember that you can parallelise this by using strategy.matrix + - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2d20d644..713dc3e7 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -1,4 +1,4 @@ -name: Test successful pipeline download with 'nf-core download' +name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually @@ -8,7 +8,7 @@ on: workflow_dispatch: inputs: testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core download." + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." required: true default: "dev" pull_request: @@ -39,9 +39,11 @@ jobs: with: python-version: "3.12" architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 with: - singularity-version: 3.8.3 + apptainer-version: 1.3.4 - name: Install dependencies run: | @@ -54,33 +56,64 @@ jobs: echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + - name: Make a cache directory for the container images + run: | + mkdir -p ./singularity_container_images + - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ + nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ --container-cache-utilisation 'amend' \ - --download-configuration + --download-configuration 'yes' - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }} + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + - name: Run the downloaded pipeline (stub) id: stub_run_pipeline continue-on-error: true env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline if: ${{ job.steps.stub_run_pipeline.status == failure() }} env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + + - name: Compare container image counts + run: | + if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ env.IMAGE_COUNT_INITIAL }} + final_count=${{ env.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 1fcafe88..a502573c 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: push: @@ -41,17 +41,32 @@ jobs: python-version: "3.12" architecture: "x64" + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.1.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Run nf-core pipelines lint + if: ${{ github.base_ref != 'master' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - - name: Run nf-core lint + - name: Run nf-core pipelines lint --release + if: ${{ github.base_ref == 'master' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 40acc23f..42e519bf 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 + uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 03ecfcf7..c6ba35df 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml new file mode 100644 index 00000000..e8aafe44 --- /dev/null +++ b/.github/workflows/template_version_comment.yml @@ -0,0 +1,46 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: pull_request_target + +jobs: + template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + ref: ${{ github.event.pull_request.head.sha }} + + - name: Read template version from .nf-core.yml + uses: nichmor/minimal-read-yaml@v0.0.2 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Check nf-core outdated + id: nf_core_outdated + run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} + + - name: Post nf-core template version comment + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + if: | + contains(env.OUTPUT, 'nf-core') + with: + repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} + allow-repeats: false + message: | + > [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + # diff --git a/.gitignore b/.gitignore index 5124c9ac..a42ce016 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ results/ testing/ testing* *.pyc +null/ diff --git a/.gitpod.yml b/.gitpod.yml index 105a1821..46118637 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,17 +4,14 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS vscode: extensions: # based on nf-core.nf-core-extensionpack - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code + #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code - charliermarsh.ruff # Code linter Ruff diff --git a/.nf-core.yml b/.nf-core.yml index e0b85a77..a016008e 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,17 @@ +bump_version: null +lint: null +nf_core_version: 3.0.2 +org_path: null repository_type: pipeline -nf_core_version: "2.14.1" +template: + author: Barry Digby, Nico Trummer + description: Quantification, miRNA target prediction and differential expression + analysis of circular RNAs + force: false + is_nfcore: true + name: circrna + org: nf-core + outdir: . + skip_features: null + version: 0.0.1dev +update: null diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4dc0f1dc..9e9f0e1c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - prettier@3.2.5 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "2.7.3" + rev: "3.0.3" hooks: - id: editorconfig-checker alias: ec diff --git a/CHANGELOG.md b/CHANGELOG.md index 27df403b..56e63438 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## vdev - [date] +## v0.0.1dev - [date] Initial release of nf-core/circrna, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index fb3c1f6e..0103d545 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,11 +12,11 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools diff --git a/LICENSE b/LICENSE index cbdceadb..8aa2385c 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) Barry Digby +Copyright (c) Barry Digby, Nico Trummer Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 558557f1..f5fc9571 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/circrna/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/circrna/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -67,8 +67,7 @@ nextflow run nf-core/circrna \ ``` > [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; -> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/circrna/usage) and the [parameter documentation](https://nf-co.re/circrna/parameters). @@ -80,7 +79,7 @@ For more details about the output files and reports, please refer to the ## Credits -nf-core/circrna was originally written by Barry Digby. +nf-core/circrna was originally written by Barry Digby, Nico Trummer. We thank the following people for their extensive assistance in the development of this pipeline: diff --git a/assets/schema_input.json b/assets/schema_input.json index fe551cb8..fd10663a 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/circrna/master/assets/schema_input.json", "title": "nf-core/circrna pipeline - params.input schema", "description": "Schema for the file provided with params.input", diff --git a/conf/base.config b/conf/base.config index cdf46e83..aaf44bfe 100644 --- a/conf/base.config +++ b/conf/base.config @@ -11,9 +11,9 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 @@ -27,30 +27,30 @@ process { // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config new file mode 100644 index 00000000..b4034d82 --- /dev/null +++ b/conf/igenomes_ignored.config @@ -0,0 +1,9 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for iGenomes paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Empty genomes dictionary to use when igenomes is ignored. +---------------------------------------------------------------------------------------- +*/ + +params.genomes = [:] diff --git a/conf/modules.config b/conf/modules.config index d203d2b6..d266a387 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -21,7 +21,6 @@ process { withName: FASTQC { ext.args = '--quiet' } - withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/test.config b/conf/test.config index a7c2516f..4c30298f 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,15 +10,18 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 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zXwhtT%ei{n#FzEH|C;yZ>+$!u_x#*+`=L8{b9SH^9&27u3G_Gxqxe`L2UJtdxghk z&-wzDFvLvW{chK5u3{n6GSKKy!P&C6w^IFpbD0bcp^A{{2lcLh_DXj@ybtYvc^;(2 M)78&qol`;+0Fu7JivR!s diff --git a/docs/output.md b/docs/output.md index afc2a9d2..23814600 100644 --- a/docs/output.md +++ b/docs/output.md @@ -29,16 +29,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). -![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) - -![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) - -![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) - -:::note -The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. -::: - ### MultiQC
diff --git a/docs/usage.md b/docs/usage.md index 98e72a06..de4b1c3b 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -85,9 +85,9 @@ The above pipeline run specified with a params file in yaml format: nextflow run nf-core/circrna -profile docker -params-file params.yaml ``` -with `params.yaml` containing: +with: -```yaml +```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' @@ -199,14 +199,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). -## Azure Resource Requests - -To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. -We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. - -Note that the choice of VM size depends on your quota and the overall workload during the analysis. -For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). - ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/main.nf b/main.nf index 810b3959..7b13c979 100644 --- a/main.nf +++ b/main.nf @@ -9,8 +9,6 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS @@ -20,7 +18,6 @@ nextflow.enable.dsl = 2 include { CIRCRNA } from './workflows/circrna' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_circrna_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_circrna_pipeline' - include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_circrna_pipeline' /* @@ -56,10 +53,8 @@ workflow NFCORE_CIRCRNA { CIRCRNA ( samplesheet ) - emit: multiqc_report = CIRCRNA.out.multiqc_report // channel: /path/to/multiqc_report.html - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -70,13 +65,11 @@ workflow NFCORE_CIRCRNA { workflow { main: - // // SUBWORKFLOW: Run initialisation tasks // PIPELINE_INITIALISATION ( params.version, - params.help, params.validate_params, params.monochrome_logs, args, @@ -90,7 +83,6 @@ workflow { NFCORE_CIRCRNA ( PIPELINE_INITIALISATION.out.samplesheet ) - // // SUBWORKFLOW: Run completion tasks // diff --git a/modules.json b/modules.json index 3b1e37ee..d04c0809 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", + "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { + "utils_nfschema_plugin": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a..691d4c76 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d79f1c86..d8989f48 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -26,7 +26,10 @@ process FASTQC { def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) + // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 + // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e0..4827da7a 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,35 +16,44 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 70edae4d..e9d79a07 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,17 +23,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -54,16 +51,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -83,13 +78,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -109,13 +102,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -138,22 +129,20 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -173,21 +162,18 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } test("sarscov2 single-end [fastq] - stub") { - options "-stub" - + options "-stub" when { process { """ @@ -201,12 +187,123 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } + { assert process.success }, + { assert snapshot(process.out).match() } ) } } + test("sarscov2 paired-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 interleaved [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [bam] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 multiple [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 custom_prefix - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 86f7c311..d5db3092 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,88 +1,392 @@ { - "fastqc_versions_interleaved": { + "sarscov2 custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:07.293713" + "timestamp": "2024-07-22T11:02:16.374038" }, - "fastqc_stub": { + "sarscov2 single-end [fastq] - stub": { "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:24.993809" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:31:01.425198" + "timestamp": "2024-07-22T11:03:10.93942" }, - "fastqc_versions_multiple": { + "sarscov2 interleaved [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:55.797907" + "timestamp": "2024-07-22T11:01:42.355718" }, - "fastqc_versions_bam": { + "sarscov2 paired-end [bam]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:26.795862" + "timestamp": "2024-07-22T11:01:53.276274" }, - "fastqc_versions_single": { + "sarscov2 multiple [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:27.043675" + "timestamp": "2024-07-22T11:02:05.527626" }, - "fastqc_versions_paired": { + "sarscov2 paired-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:31.188871" + }, + "sarscov2 paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:34.273566" + }, + "sarscov2 multiple [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:47.584191" + "timestamp": "2024-07-22T11:03:02.304411" }, - "fastqc_versions_custom_prefix": { + "sarscov2 single-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:19.095607" + }, + "sarscov2 interleaved [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:44.640184" + }, + "sarscov2 paired-end [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:41:14.576531" + "timestamp": "2024-07-22T11:02:53.550742" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67..6f5b867b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352f..cc0643e1 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,16 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml @@ -44,7 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - touch multiqc_plots + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc35..b16c1879 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,40 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242e..33316a7d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { @@ -17,6 +19,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +45,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +72,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd802..2fcbb5ff 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-10-02T17:51:46.317523" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-10-02T17:52:20.680978" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-10-02T17:52:09.185842" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 00000000..c537a6a3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} diff --git a/nextflow.config b/nextflow.config index 13ad97ff..7f032f1e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,6 +12,7 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' @@ -33,48 +34,27 @@ params { monochrome_logs = false hook_url = null help = false + help_full = false + show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' // Config options config_profile_name = null config_profile_description = null + custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' - // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' - validationShowHiddenParams = false - validate_params = true - + validate_params = true } // Load base.config by default for all pipelines includeConfig 'conf/base.config' -// Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} - -// Load nf-core/circrna custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/circrna.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/circrna profiles: ${params.custom_config_base}/pipeline/circrna.config") -} profiles { debug { dumpHashes = true @@ -89,7 +69,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda', 'defaults'] + conda.channels = ['conda-forge', 'bioconda'] apptainer.enabled = false } mamba { @@ -178,25 +158,25 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } -// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled -// Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' +// Load nf-core custom profiles from different Institutions +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" -// Nextflow plugins -plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} +// Load nf-core/circrna custom profiles from different institutions. +// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs +// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/circrna.config" : "/dev/null" + +// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +charliecloud.registry = 'quay.io' // Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} +includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -208,8 +188,15 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set bash options +process.shell = """\ +bash + +set -e # Exit if a tool returns a non-zero status/exit code +set -u # Treat unset variables and parameters as an error +set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute +set -C # No clobber - prevent output redirection from overwriting files. +""" // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false @@ -234,47 +221,50 @@ dag { manifest { name = 'nf-core/circrna' - author = """Barry Digby""" + author = """Barry Digby, Nico Trummer""" homePage = 'https://github.com/nf-core/circrna' description = """Quantification, miRNA target prediction and differential expression analysis of circular RNAs""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.0' - version = 'dev' + nextflowVersion = '!>=24.04.2' + version = '0.0.1dev' doi = '' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' +// Nextflow plugins +plugins { + id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } +validation { + defaultIgnoreParams = ["genomes"] + help { + enabled = true + command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + fullParameter = "help_full" + showHiddenParameter = "show_hidden" + beforeText = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m ${manifest.name} ${manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/${manifest.name}/blob/master/CITATIONS.md +""" + } + summary { + beforeText = validation.help.beforeText + afterText = validation.help.afterText } } + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index 82858e99..b24ff3db 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/circrna/master/nextflow_schema.json", "title": "nf-core/circrna pipeline parameters", "description": "Quantification, miRNA target prediction and differential expression analysis of circular RNAs", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -71,6 +71,14 @@ "fa_icon": "fas fa-ban", "hidden": true, "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." + }, + "igenomes_base": { + "type": "string", + "format": "directory-path", + "description": "The base path to the igenomes reference files", + "fa_icon": "fas fa-ban", + "hidden": true, + "default": "s3://ngi-igenomes/igenomes/" } } }, @@ -122,41 +130,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fab fa-acquisitions-incorporated", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", @@ -164,12 +137,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -245,27 +212,6 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "validationShowHiddenParams": { - "type": "boolean", - "fa_icon": "far fa-eye-slash", - "description": "Show all params when using `--help`", - "hidden": true, - "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "validationFailUnrecognisedParams": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." - }, - "validationLenientMode": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." - }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", @@ -278,19 +224,16 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" - }, - { - "$ref": "#/definitions/reference_genome_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/$defs/reference_genome_options" }, { - "$ref": "#/definitions/max_job_request_options" + "$ref": "#/$defs/institutional_config_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf index 5ee14910..aae83125 100644 --- a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf @@ -8,29 +8,25 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { fromSamplesheet } from 'plugin/nf-validation' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' -include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW TO INITIALISE PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit - help // boolean: Display help text validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args @@ -54,16 +50,10 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // - pre_help_text = nfCoreLogo(monochrome_logs) - post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) - def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " - UTILS_NFVALIDATION_PLUGIN ( - help, - workflow_command, - pre_help_text, - post_help_text, + UTILS_NFSCHEMA_PLUGIN ( + workflow, validate_params, - "nextflow_schema.json" + null ) // @@ -72,6 +62,7 @@ workflow PIPELINE_INITIALISATION { UTILS_NFCORE_PIPELINE ( nextflow_cli_args ) + // // Custom validation for pipeline parameters // @@ -80,8 +71,9 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // + Channel - .fromSamplesheet("input") + .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -91,8 +83,8 @@ workflow PIPELINE_INITIALISATION { } } .groupTuple() - .map { - validateInputSamplesheet(it) + .map { samplesheet -> + validateInputSamplesheet(samplesheet) } .map { meta, fastqs -> @@ -106,9 +98,9 @@ workflow PIPELINE_INITIALISATION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW FOR PIPELINE COMPLETION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_COMPLETION { @@ -123,7 +115,6 @@ workflow PIPELINE_COMPLETION { multiqc_report // string: Path to MultiQC report main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") // @@ -131,11 +122,18 @@ workflow PIPELINE_COMPLETION { // workflow.onComplete { if (email || email_on_fail) { - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + completionEmail( + summary_params, + email, + email_on_fail, + plaintext_email, + outdir, + monochrome_logs, + multiqc_report.toList() + ) } completionSummary(monochrome_logs) - if (hook_url) { imNotification(summary_params, hook_url) } @@ -147,9 +145,9 @@ workflow PIPELINE_COMPLETION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Check and validate pipeline parameters @@ -165,7 +163,7 @@ def validateInputSamplesheet(input) { def (metas, fastqs) = input[1..2] // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 if (!endedness_ok) { error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") } @@ -197,7 +195,6 @@ def genomeExistsError() { error(error_string) } } - // // Generate methods description for MultiQC // @@ -239,8 +236,10 @@ def methodsDescriptionText(mqc_methods_yaml) { // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + def manifest_doi = meta.manifest_map.doi.tokenize(",") + manifest_doi.each { doi_ref -> + temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + } meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) } else meta["doi_text"] = "" meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " @@ -261,3 +260,4 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } + diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ac31f28f..0fcbf7b3 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,18 +2,13 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { - take: print_version // boolean: print version dump_parameters // boolean: dump parameters @@ -26,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Print workflow version and exit on --version // if (print_version) { - log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") System.exit(0) } @@ -49,16 +44,16 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Generate version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -76,13 +71,13 @@ def getWorkflowVersion() { // Dump pipeline parameters to a JSON file // def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() } @@ -90,37 +85,40 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - Yaml parser = new Yaml() + def parser = new org.yaml.snakeyaml.Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return + } + catch (NullPointerException e) { + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.warn("Could not verify conda channel configuration.") + return null } // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index d0a926bf..a09572e5 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 14558c39..5cb7bafe 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,17 +2,13 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // -import org.yaml.snakeyaml.Yaml -import nextflow.extension.FilesEx - /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { - take: nextflow_cli_args @@ -25,23 +21,20 @@ workflow UTILS_NFCORE_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - valid_config = true + def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) valid_config = false } return valid_config @@ -52,12 +45,14 @@ def checkConfigProvided() { // def checkProfileProvided(nextflow_cli_args) { if (workflow.profile.endsWith(',')) { - error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } if (nextflow_cli_args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } } @@ -66,25 +61,21 @@ def checkProfileProvided(nextflow_cli_args) { // def workflowCitation() { def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs + def manifest_doi = workflow.manifest.doi.tokenize(",") + // Handling multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - temp_doi_ref + "\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" + manifest_doi.each { doi_ref -> + temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + } + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } // // Generate workflow version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -102,8 +93,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - Yaml yaml = new Yaml() - versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } return yaml.dumpAsMap(versions).trim() } @@ -113,8 +104,8 @@ def processVersionsFromYAML(yaml_file) { def workflowVersionToYAML() { return """ Workflow: - $workflow.manifest.name: ${getWorkflowVersion()} - Nextflow: $workflow.nextflow.version + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} """.stripIndent().trim() } @@ -122,11 +113,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions - .unique() - .map { processVersionsFromYAML(it) } - .unique() - .mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) } // @@ -134,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - for (group in summary_params.keySet()) { - def group_params = summary_params.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - for (param in group_params.keySet()) { - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + summary_params + .keySet() + .each { group -> + def group_params = summary_params.get(group) + // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    ${group}

    \n" + summary_section += "
    \n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" } - summary_section += "
    \n" } - } - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" return yaml_file_text } @@ -161,7 +154,7 @@ def paramsSummaryMultiqc(summary_params) { // nf-core logo // def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map String.format( """\n ${dashedLine(monochrome_logs)} @@ -180,7 +173,7 @@ def nfCoreLogo(monochrome_logs=true) { // Return dashed line // def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map return "-${colors.dim}----------------------------------------------------${colors.reset}-" } @@ -188,7 +181,7 @@ def dashedLine(monochrome_logs=true) { // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - Map colorcodes = [:] + def colorcodes = [:] as Map // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -200,54 +193,54 @@ def logColours(monochrome_logs=true) { colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" return colorcodes } @@ -262,14 +255,15 @@ def attachMultiqcReport(multiqc_report) { mqc_report = multiqc_report.getVal() if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") } mqc_report = mqc_report[0] } } - } catch (all) { + } + catch (Exception all) { if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") } } return mqc_report @@ -281,26 +275,35 @@ def attachMultiqcReport(multiqc_report) { def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" } def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] misc_fields['Date Started'] = workflow.start misc_fields['Date Completed'] = workflow.complete misc_fields['Pipeline script file path'] = workflow.scriptFile misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] @@ -338,39 +341,41 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Render the sendmail template def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { +new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception all) { // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") } } // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") output_tf.delete() } @@ -378,15 +383,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } @@ -395,21 +402,30 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) { + misc_fields['repository'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['commitid'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['revision'] = workflow.revision + } + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp def msg_fields = [:] msg_fields['version'] = getWorkflowVersion() @@ -434,13 +450,13 @@ def imNotification(summary_params, hook_url) { def json_message = json_template.toString() // POST - def post = new URL(hook_url).openConnection(); + def post = new URL(hook_url).openConnection() post.setRequestMethod("POST") post.setDoOutput(true) post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); + post.getOutputStream().write(json_message.getBytes("UTF-8")) + def postRC = post.getResponseCode() + if (!postRC.equals(200)) { + log.warn(post.getErrorStream().getText()) } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 00000000..4994303e --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,46 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + if(parameters_schema) { + log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) + } else { + log.info paramsSummaryLog(input_workflow) + } + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + if(parameters_schema) { + validateParameters(parameters_schema:parameters_schema) + } else { + validateParameters() + } + } + + emit: + dummy_emit = true +} + diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 00000000..f7d9f028 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,35 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 00000000..842dc432 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 00000000..0907ac58 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json similarity index 95% rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 7626c1c9..331e0d2f 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf deleted file mode 100644 index 2585b65d..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ /dev/null @@ -1,62 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsHelp } from 'plugin/nf-validation' -include { paramsSummaryLog } from 'plugin/nf-validation' -include { validateParameters } from 'plugin/nf-validation' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow UTILS_NFVALIDATION_PLUGIN { - - take: - print_help // boolean: print help - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log - validate_params // boolean: validate parameters - schema_filename // path: JSON schema file, null to use default value - - main: - - log.debug "Using schema file: ${schema_filename}" - - // Default values for strings - pre_help_text = pre_help_text ?: '' - post_help_text = post_help_text ?: '' - workflow_command = workflow_command ?: '' - - // - // Print help message if needed - // - if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters(parameters_schema: schema_filename) - } - - emit: - dummy_emit = true -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml deleted file mode 100644 index 3d4a6b04..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFVALIDATION_PLUGIN" -description: Use nf-validation to initiate and validate a pipeline -keywords: - - utility - - pipeline - - initialise - - validation -components: [] -input: - - print_help: - type: boolean - description: | - Print help message and exit - - workflow_command: - type: string - description: | - The command to run the workflow e.g. "nextflow run main.nf" - - pre_help_text: - type: string - description: | - Text to print before the help message - - post_help_text: - type: string - description: | - Text to print after the help message - - validate_params: - type: boolean - description: | - Validate the parameters and error if invalid. - - schema_filename: - type: string - description: | - The filename of the schema to validate against. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test deleted file mode 100644 index 5784a33f..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ /dev/null @@ -1,200 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NFVALIDATION_PLUGIN" - script "../main.nf" - workflow "UTILS_NFVALIDATION_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" - - test("Should run nothing") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should run help") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with command") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with extra text") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = "pre-help-text" - post_help_text = "post-help-text" - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('pre-help-text') } }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } }, - { assert workflow.stdout.any { it.contains('post-help-text') } } - ) - } - } - - test("Should validate params") { - - when { - - params { - monochrome_logs = true - test_data = '' - outdir = 1 - } - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = true - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cfff..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/circrna.nf b/workflows/circrna.nf index da558a8e..1f63f055 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -3,10 +3,9 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - include { FASTQC } from '../modules/nf-core/fastqc/main' include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMap } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_circrna_pipeline' @@ -21,12 +20,10 @@ workflow CIRCRNA { take: ch_samplesheet // channel: samplesheet read in from --input - main: ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() - // // MODULE: Run FastQC // @@ -42,11 +39,12 @@ workflow CIRCRNA { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_pipeline_software_mqc_versions.yml', + name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } + // // MODULE: MultiQC // @@ -62,15 +60,14 @@ workflow CIRCRNA { summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - + ch_multiqc_files = ch_multiqc_files.mix( + ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) ch_methods_description = Channel.value( methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) ch_multiqc_files = ch_multiqc_files.mix( ch_methods_description.collectFile( @@ -83,12 +80,14 @@ workflow CIRCRNA { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) - emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] + } /* From 94859e7ac11796a5de98fc907b67811196dc66a6 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Wed, 4 Dec 2024 19:51:24 +0100 Subject: [PATCH 31/32] added rRNA correlation analysis --- modules.json | 5 + .../benchmarking/decompress_reads/main.nf | 20 ++ .../benchmarking/plot_polyatails/main.nf | 14 + .../plot_polyatails/templates/create_plots.py | 47 +++ .../local/benchmarking/polyatailor/main.nf | 20 ++ .../polyatailor/templates/polyatailor.R | 73 ++++ .../benchmarking/rRNA_correlation/main.nf | 17 + .../rRNA_correlation/templates/rRNA_corr.py | 114 +++++++ .../subread/featurecounts/environment.yml | 5 + modules/nf-core/subread/featurecounts/main.nf | 57 ++++ .../nf-core/subread/featurecounts/meta.yml | 62 ++++ .../subread/featurecounts/tests/main.nf.test | 155 +++++++++ .../featurecounts/tests/main.nf.test.snap | 323 ++++++++++++++++++ .../featurecounts/tests/nextflow.config | 9 + .../subread/featurecounts/tests/tags.yml | 2 + subworkflows/local/benchmarking.nf | 87 ++++- variables_output.txt | 0 workflows/circrna/main.nf | 6 +- 18 files changed, 1013 insertions(+), 3 deletions(-) create mode 100644 modules/local/benchmarking/decompress_reads/main.nf create mode 100644 modules/local/benchmarking/plot_polyatails/main.nf create mode 100644 modules/local/benchmarking/plot_polyatails/templates/create_plots.py create mode 100644 modules/local/benchmarking/polyatailor/main.nf create mode 100644 modules/local/benchmarking/polyatailor/templates/polyatailor.R create mode 100644 modules/local/benchmarking/rRNA_correlation/main.nf create mode 100644 modules/local/benchmarking/rRNA_correlation/templates/rRNA_corr.py create mode 100644 modules/nf-core/subread/featurecounts/environment.yml create mode 100644 modules/nf-core/subread/featurecounts/main.nf create mode 100644 modules/nf-core/subread/featurecounts/meta.yml create mode 100644 modules/nf-core/subread/featurecounts/tests/main.nf.test create mode 100644 modules/nf-core/subread/featurecounts/tests/main.nf.test.snap create mode 100644 modules/nf-core/subread/featurecounts/tests/nextflow.config create mode 100644 modules/nf-core/subread/featurecounts/tests/tags.yml create mode 100644 variables_output.txt diff --git a/modules.json b/modules.json index 5c2c28ba..79e98dcc 100644 --- a/modules.json +++ b/modules.json @@ -216,6 +216,11 @@ "git_sha": "b1b959609bda44341120aed1766329909f54b8d0", "installed_by": ["modules"] }, + "subread/featurecounts": { + "branch": "master", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "installed_by": ["modules"] + }, "trimgalore": { "branch": "master", "git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a", diff --git a/modules/local/benchmarking/decompress_reads/main.nf b/modules/local/benchmarking/decompress_reads/main.nf new file mode 100644 index 00000000..6f88e3bf --- /dev/null +++ b/modules/local/benchmarking/decompress_reads/main.nf @@ -0,0 +1,20 @@ + + +process DECOMPRESS_READS { + input: + tuple val(meta), path(fastq_gz_1), path(fastq_gz_2) + + output: + tuple val(meta), path("*.fq") + + script: + """ + # Define output names by removing .gz and adding _decompressed.fq + output_name1=\$(basename ${fastq_gz_1} .gz)_decompressed.fq + output_name2=\$(basename ${fastq_gz_2} .gz)_decompressed.fq + + # Decompress the files + gunzip -c ${fastq_gz_1} > \$output_name1 + gunzip -c ${fastq_gz_2} > \$output_name2 + """ +} diff --git a/modules/local/benchmarking/plot_polyatails/main.nf b/modules/local/benchmarking/plot_polyatails/main.nf new file mode 100644 index 00000000..26f173f6 --- /dev/null +++ b/modules/local/benchmarking/plot_polyatails/main.nf @@ -0,0 +1,14 @@ +process PLOT_POLYATAILS { + label "process_single" + + conda "bioconda::seaborn=0.11.2" + container 'community.wave.seqera.io/library/seaborn:0.13.2--ef0811a05c6fcc75' + + input: + path(real) + path(benchmarking) + output: + path("*.tsv") , emit: average_tails + script: + template "create_plots.py" +} \ No newline at end of file diff --git a/modules/local/benchmarking/plot_polyatails/templates/create_plots.py b/modules/local/benchmarking/plot_polyatails/templates/create_plots.py new file mode 100644 index 00000000..dcf2afc6 --- /dev/null +++ b/modules/local/benchmarking/plot_polyatails/templates/create_plots.py @@ -0,0 +1,47 @@ +#!/usr/bin/env python3 +import csv +import matplotlib.pyplot as plt +import seaborn as sns +import pandas as pd +import platform + +# Function to calculate the average nA value for a given file +def calculate_average_na(file_path): + # Read the TSV file into a pandas DataFrame + df = pd.read_csv(file_path, sep='\t') # Use tab as the separator + + # Calculate the mean of the nA column + avg_na = df['nA'].mean() + + # Extract the sample name from the 'sample' column (since all rows have the same sample) + sample_name = df['sample'].iloc[0] + + return avg_na, sample_name + +def main(file_list, output_file): + # Initialize lists to store the averages and corresponding samples + averages = [] + samples = [] + + # Loop through each file in the list + for file_path in file_list: + avg_na, sample_name = calculate_average_na(file_path) + averages.append(avg_na) + samples.append(sample_name) + + # Write the results to a TSV file + with open(output_file, 'w', newline='') as tsvfile: + writer = csv.writer(tsvfile, delimiter='\t') # Tab-separated output + writer.writerow(['sample', 'avg']) # Write header + for sample, avg in zip(samples, averages): + writer.writerow([sample, avg]) + +if __name__ == "__main__": + file_list_r = '$real'.split(' ') + output_file_r = 'real.tsv' + main(file_list_r, output_file_r) + file_list_b = '$benchmarking'.split(' ') + output_file_b = 'benchmarking.tsv' + main(file_list_b, output_file_b) + + \ No newline at end of file diff --git a/modules/local/benchmarking/polyatailor/main.nf b/modules/local/benchmarking/polyatailor/main.nf new file mode 100644 index 00000000..3427728d --- /dev/null +++ b/modules/local/benchmarking/polyatailor/main.nf @@ -0,0 +1,20 @@ +process POLYATAILOR { + tag "$meta.id" + label "process_high" + + container 'docker://faboehm/polyatailor-env' + + input: + tuple val(meta), + path(fastq) + path(bam) + + output: + path("*.tsv"), emit: tails + path("versions.yml"), emit: versions + + script: + template'polyatailor.R' + +} + diff --git a/modules/local/benchmarking/polyatailor/templates/polyatailor.R b/modules/local/benchmarking/polyatailor/templates/polyatailor.R new file mode 100644 index 00000000..fc8e3d6f --- /dev/null +++ b/modules/local/benchmarking/polyatailor/templates/polyatailor.R @@ -0,0 +1,73 @@ +#!/usr/bin/env Rscript +library(PolyAtailor) +library(Biostrings) +library(yaml) # To write the YAML file +library(Rsamtools) # Ensure Rsamtools is loaded for scanBam +library(GenomicAlignments) +library(dplyr) +conflict_prefer("filter", "dplyr") +conflict_prefer("rename", "dplyr") +conflict_prefer("strsplit", "base") + +fastq_string <- '$fastq' +fastq_files <- unlist(strsplit(fastq_string, " ")) +sample_names <- gsub(".fq.gz\$", "", fastq_files) + +result_1 <- tailScan( + fastq = fastq_files[1], + mcans = 3, + findUmi = FALSE, + lumi = 0, + adapterSeq = "", + anchorSeq = "", + resultpath = "./", + samplename = sample_names[1], + tailAnchorLen = 8, + minTailLen = 5, + realTailLen = 15, + maxNtail = 2, + mapping = FALSE, + mapinfo = NULL, + findTailType = 'A' +) + +write.table(result_1, file = paste0(sample_names[1], ".tsv"), sep = "\t", row.names = FALSE, col.names = TRUE) + +result_2 <- tailScan( + fastq = fastq_files[2], + mcans = 3, + findUmi = FALSE, + lumi = 0, + adapterSeq = "", + anchorSeq = "", + resultpath = "./", + samplename = sample_names[2], + tailAnchorLen = 8, + minTailLen = 5, + realTailLen = 15, + maxNtail = 2, + mapping = FALSE, + mapinfo = NULL, + findTailType = 'A' +) +write.table(result_2, file = paste0(sample_names[2], ".tsv"), sep = "\t", row.names = FALSE, col.names = TRUE) + +result_tailMap <- tailMap( + bamfile = '$bam', + mcans = 3, + minTailLen = 5, + findUmi = FALSE, + maxNtail = 2, + mapping = TRUE, + longRead = FALSE +) +write.csv(result_tailMap, "map.csv", row.names = FALSE) + + + +version_info <- list( + PolyAtailor_version = as.character(packageVersion("PolyAtailor")), + Biostrings_version = as.character(packageVersion("Biostrings")), + run_time = Sys.time() +) +write_yaml(version_info, "versions.yml") diff --git a/modules/local/benchmarking/rRNA_correlation/main.nf b/modules/local/benchmarking/rRNA_correlation/main.nf new file mode 100644 index 00000000..221d779c --- /dev/null +++ b/modules/local/benchmarking/rRNA_correlation/main.nf @@ -0,0 +1,17 @@ +process RRNA_CORRELATION { + label "process_single" + + conda "bioconda::pandas=1.5.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'biocontainers/pandas:1.5.2' }" + + input: + val bed_real_list // Collected list of tuples for real BEDs + val bed_bench_list // Collected list of tuples for benchmarking BEDs + val rRNA_real_list // Collected list of tuples for real rRNA summaries + val rRNA_bench_list // Collected list of tuples for benchmarking rRNA summaries + + script: + template "rRNA_corr.py" +} diff --git a/modules/local/benchmarking/rRNA_correlation/templates/rRNA_corr.py b/modules/local/benchmarking/rRNA_correlation/templates/rRNA_corr.py new file mode 100644 index 00000000..fc0c46bd --- /dev/null +++ b/modules/local/benchmarking/rRNA_correlation/templates/rRNA_corr.py @@ -0,0 +1,114 @@ +#!/usr/bin/env python3 +import numpy as np +from collections import defaultdict + +def process_meta_and_paths(input_string): + # 1. Strip the first and last character + stripped_input = input_string.replace("[[", "[").replace("]]", "]") + + # 2. Split by "[", resulting in a list + split_data = stripped_input.split("[") + + # 3. For every list member, strip all occurrences of "]" + cleaned_data = [item.replace("]", "").strip() for item in split_data if item.strip()] + + # 4. For every list member, split by "," + parsed_data = [item.split(",") for item in cleaned_data] + + parsed_data = [sublist[:-1] if sublist[-1] == '' else sublist for sublist in parsed_data] + + + return parsed_data + + +def calculate_favcount_summary_ratio(file_path): + with open(file_path.strip(), 'r') as file: + lines = file.readlines() + assigned = int(lines[1].split()[1]) + unassigned_multimapping = int(lines[9].split()[1]) + others_sum = sum(int(lines[i].split()[1]) for i in list(range(2, 9)) + list(range(10, 15))) + ratio = (assigned + unassigned_multimapping) + #others_sum if others_sum != 0 else 1 + return ratio + + + +def getpairs (beds, favcounts): + pairs = [] + for bed in beds: + fav = None + for f in favcounts: + if f[0] == bed[0]: + fav = f + break + pairs.append([bed[0],bed[4],bed[-1],fav[-1]]) + return pairs + +def get_totals(pairs): + for i in range(len(pairs)): + bed = pairs[i][2].strip(" ") + fav = pairs[i][3] + with open(bed, 'r') as file: + bed_value = sum(1 for line in file) + pairs[i][2] = bed_value + pairs[i][3] = calculate_favcount_summary_ratio(fav) + return pairs + + +def sort_tools(value_pairs): + grouped_data = defaultdict(list) + for entry in value_pairs: + grouped_data[entry[1]].append(entry) + return dict(grouped_data) + + +def compute_correlation(value_pairs): + results = defaultdict(float) + for tool in value_pairs.keys(): + bed_list, fav_list = zip(*[sublist[2:] for sublist in value_pairs[tool]]) + correlation = np.corrcoef(bed_list, fav_list)[0,1] + results[tool] = correlation + return dict(results) + + + + +# Input data from Nextflow variables +real_bed = "$bed_real_list" +bench_bed = "$bed_bench_list" +real_rRNA = "$rRNA_real_list" +bench_rRNA = "$rRNA_bench_list" + +real_bed = process_meta_and_paths(real_bed) +bench_bed = process_meta_and_paths(bench_bed) +real_rRNA = process_meta_and_paths(real_rRNA) +bench_rRNA = process_meta_and_paths(bench_rRNA) + +real_pairs = getpairs(real_bed,real_rRNA) +bench_pairs = getpairs(bench_bed,bench_rRNA) + + +real_value_pairs = get_totals(real_pairs) +bench_value_pairs = get_totals(bench_pairs) + +real_value_pairs = sort_tools(real_value_pairs) +bench_value_pairs = sort_tools(bench_value_pairs) + +real_corr = compute_correlation(real_value_pairs) +bench_corr = compute_correlation(bench_value_pairs) + +with open("real_corr.txt", "w") as file: + for key, value in real_corr.items(): + # Remove leading space in the key if required + line = f"{key.strip()}:\\t{value}\\n" + file.write(line) + +with open("bench_corr.txt", "w") as file: + for key, value in bench_corr.items(): + # Remove leading space in the key if required + line = f"{key.strip()}:\\t{value}\\n" + file.write(line) + +#TODO: both relative or both total. both? +#TODO: both correllations the same can't be!!! + diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml new file mode 100644 index 00000000..fdb57502 --- /dev/null +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::subread=2.0.6 diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf new file mode 100644 index 00000000..c0c9de4d --- /dev/null +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -0,0 +1,57 @@ +process SUBREAD_FEATURECOUNTS { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container 'oras://community.wave.seqera.io/library/subread:2.0.6--2dd2dd526de026fd' + + input: + tuple val(meta), path(bams), path(annotation) + + output: + tuple val(meta), path("*featureCounts.txt") , emit: counts + tuple val(meta), path("*featureCounts.txt.summary"), emit: summary + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def paired_end = meta.single_end ? '' : '-p' + + def strandedness = 0 + if (meta.strandedness == 'forward') { + strandedness = 1 + } else if (meta.strandedness == 'reverse') { + strandedness = 2 + } + """ + featureCounts \\ + $args \\ + $paired_end \\ + -T $task.cpus \\ + -a $annotation \\ + -s $strandedness \\ + -o ${prefix}.featureCounts.txt \\ + ${bams.join(' ')} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + subread: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g") + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.featureCounts.txt + touch ${prefix}.featureCounts.txt.summary + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + subread: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/subread/featurecounts/meta.yml b/modules/nf-core/subread/featurecounts/meta.yml new file mode 100644 index 00000000..a9b045b7 --- /dev/null +++ b/modules/nf-core/subread/featurecounts/meta.yml @@ -0,0 +1,62 @@ +name: subread_featurecounts +description: Count reads that map to genomic features +keywords: + - counts + - fasta + - genome + - reference +tools: + - featurecounts: + description: featureCounts is a highly efficient general-purpose read summarization + program that counts mapped reads for genomic features such as genes, exons, + promoter, gene bodies, genomic bins and chromosomal locations. It can be used + to count both RNA-seq and genomic DNA-seq reads. + homepage: http://bioinf.wehi.edu.au/featureCounts/ + documentation: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf + doi: "10.1093/bioinformatics/btt656" + licence: ["GPL v3"] + identifier: biotools:subread +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: BAM files containing mapped reads + pattern: "*.bam" + - annotation: + type: file + description: Genomic features annotation in GTF or SAF + pattern: "*.{gtf,saf}" +output: + - counts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*featureCounts.txt": + type: file + description: Counts of reads mapping to features + pattern: "*featureCounts.txt" + - summary: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*featureCounts.txt.summary": + type: file + description: Summary log file + pattern: "*.featureCounts.txt.summary" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@ntoda03" +maintainers: + - "@ntoda03" diff --git a/modules/nf-core/subread/featurecounts/tests/main.nf.test b/modules/nf-core/subread/featurecounts/tests/main.nf.test new file mode 100644 index 00000000..3b95da33 --- /dev/null +++ b/modules/nf-core/subread/featurecounts/tests/main.nf.test @@ -0,0 +1,155 @@ +nextflow_process { + + name "Test Process SUBREAD_FEATURECOUNTS" + script "../main.nf" + process "SUBREAD_FEATURECOUNTS" + config "./nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "subread" + tag "subread/featurecounts" + + test("sarscov2 [bam] - forward") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true, strandedness:'forward' ], // meta map + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.counts).match("forward_counts") }, + { assert snapshot(process.out.summary).match("forward_summary") }, + { assert snapshot(process.out.versions).match("forward_versions") } + ) + } + } + + test("sarscov2 [bam] - forward - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true, strandedness:'forward' ], // meta map + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 [bam] - reverse") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true, strandedness:'reverse' ], // meta map + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.counts).match("reverse_counts") }, + { assert snapshot(process.out.summary).match("reverse_summary") }, + { assert snapshot(process.out.versions).match("reverse_versions") } + ) + } + } + + test("sarscov2 [bam] - reverse - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true, strandedness:'reverse' ], // meta map + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 [bam] - unstranded") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.counts).match("unstranded_counts") }, + { assert snapshot(process.out.summary).match("unstranded_summary") }, + { assert snapshot(process.out.versions).match("unstranded_versions") } + ) + } + } + + test("sarscov2 [bam] - unstranded - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap new file mode 100644 index 00000000..5a743f0c --- /dev/null +++ b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap @@ -0,0 +1,323 @@ +{ + "forward_counts": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "forward" + }, + "test.featureCounts.txt:md5,4cf89f0e702ba9abef3fa571e68fe8f0" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:19:47.695388295" + }, + "unstranded_counts": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "unstranded" + }, + "test.featureCounts.txt:md5,c4ef2c2a80547fbb3074331bc0a1bda3" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:21:03.208334705" + }, + "reverse_summary": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "reverse" + }, + "test.featureCounts.txt.summary:md5,7cfa30ad678b9bc1bc63afbb0281547b" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-11-23T15:50:25.168206514" + }, + "sarscov2 [bam] - forward - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "forward" + }, + "test.featureCounts.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "forward" + }, + "test.featureCounts.txt.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" + ], + "counts": [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "forward" + }, + "test.featureCounts.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary": [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "forward" + }, + "test.featureCounts.txt.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:20:10.040191252" + }, + "sarscov2 [bam] - reverse - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "reverse" + }, + "test.featureCounts.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "reverse" + }, + "test.featureCounts.txt.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" + ], + "counts": [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "reverse" + }, + "test.featureCounts.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary": [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "reverse" + }, + "test.featureCounts.txt.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:20:42.708101743" + }, + "reverse_counts": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "reverse" + }, + "test.featureCounts.txt:md5,a7d8843ebc12d855c2e68d3e2e137582" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:20:24.490755916" + }, + "sarscov2 [bam] - unstranded - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "unstranded" + }, + "test.featureCounts.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "unstranded" + }, + "test.featureCounts.txt.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" + ], + "counts": [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "unstranded" + }, + "test.featureCounts.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary": [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "unstranded" + }, + "test.featureCounts.txt.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:21:19.244837771" + }, + "forward_summary": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "forward" + }, + "test.featureCounts.txt.summary:md5,8f602ff9a8ef467af43294e80b367cdf" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-11-23T15:50:10.699024934" + }, + "forward_versions": { + "content": [ + [ + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:19:48.001158764" + }, + "unstranded_summary": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true, + "strandedness": "unstranded" + }, + "test.featureCounts.txt.summary:md5,23164b79f9f23f11c82820db61a35560" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-11-23T15:50:38.68776235" + }, + "reverse_versions": { + "content": [ + [ + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:20:24.551053149" + }, + "unstranded_versions": { + "content": [ + [ + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:21:03.25895568" + } +} \ No newline at end of file diff --git a/modules/nf-core/subread/featurecounts/tests/nextflow.config b/modules/nf-core/subread/featurecounts/tests/nextflow.config new file mode 100644 index 00000000..d9fd4fd5 --- /dev/null +++ b/modules/nf-core/subread/featurecounts/tests/nextflow.config @@ -0,0 +1,9 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: SUBREAD_FEATURECOUNTS { + ext.args = '-t CDS' + } + +} diff --git a/modules/nf-core/subread/featurecounts/tests/tags.yml b/modules/nf-core/subread/featurecounts/tests/tags.yml new file mode 100644 index 00000000..6d2534bf --- /dev/null +++ b/modules/nf-core/subread/featurecounts/tests/tags.yml @@ -0,0 +1,2 @@ +subread/featurecounts: + - modules/nf-core/subread/featurecounts/** diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf index 09fbda3d..7df2181f 100644 --- a/subworkflows/local/benchmarking.nf +++ b/subworkflows/local/benchmarking.nf @@ -3,28 +3,111 @@ include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge include { BEDTOOLS_INTERSECT } from '../../modules/nf-core/bedtools/intersect' include { BEDTOOLS_JACCARD } from '../../modules/nf-core/bedtools/jaccard' include { BEDTOOLS_GENOMECOV } from '../../modules/nf-core/bedtools/genomecov' -include { BENCHMARKING_MULTIQC as JACCARD_MULTIQC } from '../../modules/local/benchmarking/multiqc' +include { BENCHMARKING_MULTIQC as JACCARD_MULTIQC } from '../../modules/local/benchmarking/multiqc' include { BENCHMARKING_MULTIQC as CORRELATION_MULTIQC } from '../../modules/local/benchmarking/multiqc' include { PNG_JSON as LOCATION_JSON } from '../../modules/local/benchmarking/png_json' include { PNG_JSON as OVERLAP_JSON } from '../../modules/local/benchmarking/png_json' include { LOCATION_PLOT } from '../../modules/local/benchmarking/location_plots' include { OVERLAP_PLOT } from '../../modules/local/benchmarking/overlap_plot' include { SEQ_DEPTH_CORRELLATION } from '../../modules/local/benchmarking/seq_depth_plot' -include { AVERAGE_TSV } from '../../modules/local/benchmarking/average_tsv' +include { AVERAGE_TSV } from '../../modules/local/benchmarking/average_tsv' +include { POLYATAILOR as POLYATAILOR_REAL } from '../../modules/local/benchmarking/polyatailor' +include { POLYATAILOR as POLYATAILOR_BENCHMARK} from '../../modules/local/benchmarking/polyatailor' +include { PLOT_POLYATAILS } from '../../modules/local/benchmarking/plot_polyatails' +include { SUBREAD_FEATURECOUNTS as FEATURECOUNTS_TOTAL } from '../../modules/nf-core/subread/featurecounts' +include { SUBREAD_FEATURECOUNTS as FEATURECOUNTS_BENCHMARKING} from '../../modules/nf-core/subread/featurecounts' +include { STAR2PASS as STAR2PASS_REAL } from './detection_tools/star2pass' +include { STAR2PASS as STAR2PASS_BENCHMARKING } from './detection_tools/star2pass' +include { STAR_GENOMEGENERATE } from '../../modules/nf-core/star/genomegenerate' +include { DECOMPRESS_READS as DECOMPRESS_REAL } from '../../modules/local/benchmarking/decompress_reads' +include { DECOMPRESS_READS as DECOMPRESS_BENCHMARKING} from '../../modules/local/benchmarking/decompress_reads' +include { RRNA_CORRELATION } from '../../modules/local/benchmarking/rRNA_correlation' workflow BENCHMARKING { take: + ch_reads_real + ch_reads_benchmarking ch_real_bed ch_benchmarking_bed ch_real_bam ch_benchmarking_bam ch_trim_report + ch_fasta + bsj_reads main: + //quality score estimation + /*ch_reads_benchmarking.view {"rb: $it"} + ch_reads_real.view {"rr: $it"} + ch_polya_real = POLYATAILOR_REAL(ch_reads_real, ch_real_bam.map { it[1] }) + ch_polya_benchmarking = POLYATAILOR_BENCHMARK(ch_reads_benchmarking, ch_benchmarking_bam.map { it[1] }) + + ch_polya_real.tails.collect().view {"pr: $it"} + ch_polya_benchmarking.tails.collect().view {"pb: $it"} + + ch_polya_plots = PLOT_POLYATAILS(ch_polya_real.tails.collect(), ch_polya_benchmarking.tails.collect()) + ch_polya_plots.average_tails.view {"$it"}*/ + + + // Use only the paths in each tuple of ch_reads_real and ch_reads_benchmarking, assuming the metadata is already present + // Define parameters + ch_benchmark_gtf = "/nfs/data3/CIRCEST/runs/test_benchmarking/gencode.v47.primary_assembly.annotation.gtf" + ch_benchmarking_fasta = "/nfs/data3/CIRCEST/runs/test_benchmarking/gencode.v47.rRNARNA_transcripts.fa" + ch_filter_gtf = "/nfs/data3/CIRCEST/runs/test_benchmarking/ensembl_rRNA.gtf" + + STAR_GENOMEGENERATE(ch_fasta, tuple([id: "benchmarking_gtf"], file(ch_benchmark_gtf))) + star_index = params.star ? Channel.value([[id: "star"], file(params.star, checkIfExists: true)]) : STAR_GENOMEGENERATE.out.index.collect() + star_ignore_sjdbgtf = true + seq_center = params.seq_center ?: '' + seq_platform = '' + + + ch_reads_real_restructured = ch_reads_real.map { meta, fastq_gz_list -> + tuple(meta, fastq_gz_list[0], fastq_gz_list[1]) + } + ch_reads_benchmarking_restructured = ch_reads_benchmarking.map { meta, fastq_gz_list -> + tuple(meta, fastq_gz_list[0], fastq_gz_list[1]) + } + ch_uncompressed_reads_real = DECOMPRESS_REAL(ch_reads_real_restructured) + ch_uncompressed_reads_benchmarking = DECOMPRESS_BENCHMARKING(ch_reads_benchmarking_restructured) + + ch_rRNA_real_bam = STAR2PASS_REAL(ch_uncompressed_reads_real, star_index, tuple([id: "Benchmarking_gtf"], file(ch_benchmark_gtf)), bsj_reads, star_ignore_sjdbgtf, seq_center, seq_platform).bam + + ch_rRNA_benchmarking_bam = STAR2PASS_BENCHMARKING(ch_uncompressed_reads_benchmarking, star_index, tuple([id: "Benchmarking_gtf"], file(ch_benchmark_gtf)), bsj_reads, star_ignore_sjdbgtf, seq_center, seq_platform).bam + + + + ch_rRNA_real_input = ch_real_bam.map { meta, path -> + tuple(meta, path, file(ch_filter_gtf)) + } + ch_rRNA_benchmarking_input = ch_benchmarking_bam.map { meta, path -> + tuple(meta, path, file(ch_filter_gtf)) + } + + ch_rRNA_real = FEATURECOUNTS_TOTAL(ch_rRNA_real_input).summary + ch_rRNA_benchmarking = FEATURECOUNTS_BENCHMARKING(ch_rRNA_benchmarking_input).summary + + + ch_collected_real_bed = ch_real_bed.collect() + ch_collected_benchmarking_bed = ch_benchmarking_bed.collect() + ch_collected_rRNA_real = ch_rRNA_real.collect() + ch_collected_rRNA_benchmarking = ch_rRNA_benchmarking.collect() + + RRNA_CORRELATION( + ch_collected_real_bed, + ch_collected_benchmarking_bed, + ch_collected_rRNA_real, + ch_collected_rRNA_benchmarking + ) + + + //ch_rRNA_benchmarking.view { "bench: $it" } + + //data preparation ch_versions = Channel.empty() diff --git a/variables_output.txt b/variables_output.txt new file mode 100644 index 00000000..e69de29b diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index b656bd01..3713e38e 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -182,11 +182,15 @@ workflow CIRCRNA { ) BENCHMARKING( + ch_reads.real, + ch_reads.benchmarking, BSJ_DETECTION.out.bed_per_sample_tool, BSJ_DETECTION_BENCHMARKING.out.bed_per_sample_tool, BSJ_DETECTION.out.star_bam, BSJ_DETECTION_BENCHMARKING.out.star_bam, - FASTQC_TRIMGALORE.out.trim_log + FASTQC_TRIMGALORE.out.trim_log, + ch_fasta, + params.bsj_reads ) ch_multiqc_files = ch_multiqc_files.mix(BENCHMARKING.out.reports) From 80c16284d07893595349a21c937866cfab84c7a3 Mon Sep 17 00:00:00 2001 From: Fabian Boehm Date: Wed, 4 Dec 2024 21:05:10 +0100 Subject: [PATCH 32/32] Template update for nf-core/tools version 2.14.1 --- .github/CONTRIBUTING.md | 12 +- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 25 +- .github/workflows/ci.yml | 57 +-- .github/workflows/download_pipeline.yml | 53 +-- .github/workflows/linting.yml | 23 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 2 +- .../workflows/template_version_comment.yml | 46 --- .gitignore | 1 - .gitpod.yml | 7 +- .nf-core.yml | 17 +- .pre-commit-config.yaml | 2 +- CHANGELOG.md | 2 +- CITATIONS.md | 4 +- LICENSE | 2 +- README.md | 7 +- assets/schema_input.json | 2 +- conf/base.config | 34 +- conf/igenomes_ignored.config | 9 - conf/modules.config | 1 + conf/test.config | 13 +- docs/images/mqc_fastqc_adapter.png | Bin 0 -> 23458 bytes docs/images/mqc_fastqc_counts.png | Bin 0 -> 33918 bytes docs/images/mqc_fastqc_quality.png | Bin 0 -> 55769 bytes docs/output.md | 10 + docs/usage.md | 12 +- main.nf | 8 + modules.json | 12 +- modules/nf-core/fastqc/environment.yml | 2 + modules/nf-core/fastqc/main.nf | 5 +- modules/nf-core/fastqc/meta.yml | 57 ++- modules/nf-core/fastqc/tests/main.nf.test | 225 +++-------- .../nf-core/fastqc/tests/main.nf.test.snap | 370 ++---------------- modules/nf-core/multiqc/environment.yml | 4 +- modules/nf-core/multiqc/main.nf | 16 +- modules/nf-core/multiqc/meta.yml | 78 ++-- modules/nf-core/multiqc/tests/main.nf.test | 8 - .../nf-core/multiqc/tests/main.nf.test.snap | 24 +- modules/nf-core/multiqc/tests/nextflow.config | 5 - nextflow.config | 148 +++---- nextflow_schema.json | 85 +++- .../utils_nfcore_circrna_pipeline/main.nf | 66 ++-- .../nf-core/utils_nextflow_pipeline/main.nf | 70 ++-- .../tests/nextflow.config | 2 +- .../nf-core/utils_nfcore_pipeline/main.nf | 306 +++++++-------- .../nf-core/utils_nfschema_plugin/main.nf | 46 --- .../nf-core/utils_nfschema_plugin/meta.yml | 35 -- .../utils_nfschema_plugin/tests/main.nf.test | 117 ------ .../tests/nextflow.config | 8 - .../nf-core/utils_nfvalidation_plugin/main.nf | 62 +++ .../utils_nfvalidation_plugin/meta.yml | 44 +++ .../tests/main.nf.test | 200 ++++++++++ .../tests/nextflow_schema.json | 8 +- .../utils_nfvalidation_plugin/tests/tags.yml | 2 + workflows/circrna.nf | 21 +- 56 files changed, 969 insertions(+), 1410 deletions(-) delete mode 100644 .github/workflows/template_version_comment.yml delete mode 100644 conf/igenomes_ignored.config create mode 100755 docs/images/mqc_fastqc_adapter.png create mode 100755 docs/images/mqc_fastqc_counts.png create mode 100755 docs/images/mqc_fastqc_quality.png delete mode 100644 modules/nf-core/multiqc/tests/nextflow.config delete mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf delete mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml delete mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test delete mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test rename subworkflows/nf-core/{utils_nfschema_plugin => utils_nfvalidation_plugin}/tests/nextflow_schema.json (95%) create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index ff849d6c..d8a9ab91 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/circrna, the standard workflow is a 1. Check that there isn't already an issue about your idea in the [nf-core/circrna issues](https://github.com/nf-core/circrna/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/circrna repository](https://github.com/nf-core/circrna) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). @@ -40,7 +40,7 @@ There are typically two types of tests that run: ### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. @@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards: 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. @@ -86,11 +86,11 @@ If you wish to contribute a new step, please use the following coding standards: Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. -Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. +Once there, use `nf-core schema build` to add to `nextflow_schema.json`. ### Default processes resource requirements -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. @@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g ### Nextflow version bumping -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` ### Images and figures diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 187fef97..9d44ed38 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/circ - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/circrna/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/circrna _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. -- [ ] Make sure your code lints (`nf-core pipelines lint`). +- [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 59013de0..8f7ea0eb 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,35 +1,18 @@ name: nf-core AWS full size tests -# This workflow is triggered on PRs opened against the master branch. +# This workflow is triggered on published releases. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: - pull_request: - branches: - - master + release: + types: [published] workflow_dispatch: - pull_request_review: - types: [submitted] - jobs: run-platform: name: Run AWS full tests - # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered - if: github.repository == 'nf-core/circrna' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' + if: github.repository == 'nf-core/circrna' runs-on: ubuntu-latest steps: - - uses: octokit/request-action@v2.x - id: check_approvals - with: - route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - - id: test_variables - if: github.event_name != 'workflow_dispatch' - run: | - JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' - CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') - test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index bb52ff21..8bfcd749 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,12 +7,9 @@ on: pull_request: release: types: [published] - workflow_dispatch: env: NXF_ANSI_LOG: false - NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity - NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" @@ -20,66 +17,30 @@ concurrency: jobs: test: - name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" + name: Run pipeline with test data # Only run on push if this is the nf-core dev branch (merged PRs) if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/circrna') }}" runs-on: ubuntu-latest strategy: matrix: NXF_VER: - - "24.04.2" + - "23.04.0" - "latest-everything" - profile: - - "conda" - - "docker" - - "singularity" - test_name: - - "test" - isMaster: - - ${{ github.base_ref == 'master' }} - # Exclude conda and singularity on dev - exclude: - - isMaster: false - profile: "conda" - - isMaster: false - profile: "singularity" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Set up Nextflow + - name: Install Nextflow uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" - - name: Set up Apptainer - if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-apptainer@main - - - name: Set up Singularity - if: matrix.profile == 'singularity' - run: | - mkdir -p $NXF_SINGULARITY_CACHEDIR - mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - - name: Set up Miniconda - if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - with: - miniconda-version: "latest" - auto-update-conda: true - conda-solver: libmamba - channels: conda-forge,bioconda - - - name: Set up Conda - if: matrix.profile == 'conda' - run: | - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH - - - name: Clean up Disk space + - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" + - name: Run pipeline with test data + # TODO nf-core: You can customise CI pipeline run tests as required + # For example: adding multiple test runs with different parameters + # Remember that you can parallelise this by using strategy.matrix run: | - nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 713dc3e7..2d20d644 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -1,4 +1,4 @@ -name: Test successful pipeline download with 'nf-core pipelines download' +name: Test successful pipeline download with 'nf-core download' # Run the workflow when: # - dispatched manually @@ -8,7 +8,7 @@ on: workflow_dispatch: inputs: testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." + description: "The specific branch you wish to utilize for the test execution of nf-core download." required: true default: "dev" pull_request: @@ -39,11 +39,9 @@ jobs: with: python-version: "3.12" architecture: "x64" - - - name: Setup Apptainer - uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 + - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 with: - apptainer-version: 1.3.4 + singularity-version: 3.8.3 - name: Install dependencies run: | @@ -56,64 +54,33 @@ jobs: echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} - - name: Make a cache directory for the container images - run: | - mkdir -p ./singularity_container_images - - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_CACHEDIR: ./ run: | - nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ + nf-core download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ + --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ --container-cache-utilisation 'amend' \ - --download-configuration 'yes' + --download-configuration - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }} - - name: Count the downloaded number of container images - id: count_initial - run: | - image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) - echo "Initial container image count: $image_count" - echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} - - name: Run the downloaded pipeline (stub) id: stub_run_pipeline continue-on-error: true env: - NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline if: ${{ job.steps.stub_run_pipeline.status == failure() }} env: - NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results - - - name: Count the downloaded number of container images - id: count_afterwards - run: | - image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) - echo "Post-pipeline run container image count: $image_count" - echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} - - - name: Compare container image counts - run: | - if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then - initial_count=${{ env.IMAGE_COUNT_INITIAL }} - final_count=${{ env.IMAGE_COUNT_AFTER }} - difference=$((final_count - initial_count)) - echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" - tree ./singularity_container_images - exit 1 - else - echo "The pipeline can be downloaded successfully!" - fi diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index a502573c..1fcafe88 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core pipelines lint` and markdown lint tests to ensure +# It runs the `nf-core lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: push: @@ -41,32 +41,17 @@ jobs: python-version: "3.12" architecture: "x64" - - name: read .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.1.0 - id: read_yml - with: - config: ${{ github.workspace }}/.nf-core.yml - - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - - - name: Run nf-core pipelines lint - if: ${{ github.base_ref != 'master' }} - env: - GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + pip install nf-core - - name: Run nf-core pipelines lint --release - if: ${{ github.base_ref == 'master' }} + - name: Run nf-core lint env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 42e519bf..40acc23f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 + uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index c6ba35df..03ecfcf7 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml deleted file mode 100644 index e8aafe44..00000000 --- a/.github/workflows/template_version_comment.yml +++ /dev/null @@ -1,46 +0,0 @@ -name: nf-core template version comment -# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. -# It posts a comment to the PR, even if it comes from a fork. - -on: pull_request_target - -jobs: - template_version: - runs-on: ubuntu-latest - steps: - - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - with: - ref: ${{ github.event.pull_request.head.sha }} - - - name: Read template version from .nf-core.yml - uses: nichmor/minimal-read-yaml@v0.0.2 - id: read_yml - with: - config: ${{ github.workspace }}/.nf-core.yml - - - name: Install nf-core - run: | - python -m pip install --upgrade pip - pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - - - name: Check nf-core outdated - id: nf_core_outdated - run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} - - - name: Post nf-core template version comment - uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 - if: | - contains(env.OUTPUT, 'nf-core') - with: - repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} - allow-repeats: false - message: | - > [!WARNING] - > Newer version of the nf-core template is available. - > - > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. - > Please update your pipeline to the latest version. - > - > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). - # diff --git a/.gitignore b/.gitignore index a42ce016..5124c9ac 100644 --- a/.gitignore +++ b/.gitignore @@ -6,4 +6,3 @@ results/ testing/ testing* *.pyc -null/ diff --git a/.gitpod.yml b/.gitpod.yml index 46118637..105a1821 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,14 +4,17 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update + - name: unset JAVA_TOOL_OPTIONS + command: | + unset JAVA_TOOL_OPTIONS vscode: extensions: # based on nf-core.nf-core-extensionpack - #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code + - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - - nextflow.nextflow # Nextflow syntax highlighting + # - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code - charliermarsh.ruff # Code linter Ruff diff --git a/.nf-core.yml b/.nf-core.yml index a016008e..e0b85a77 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,17 +1,2 @@ -bump_version: null -lint: null -nf_core_version: 3.0.2 -org_path: null repository_type: pipeline -template: - author: Barry Digby, Nico Trummer - description: Quantification, miRNA target prediction and differential expression - analysis of circular RNAs - force: false - is_nfcore: true - name: circrna - org: nf-core - outdir: . - skip_features: null - version: 0.0.1dev -update: null +nf_core_version: "2.14.1" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9e9f0e1c..4dc0f1dc 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - prettier@3.2.5 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "3.0.3" + rev: "2.7.3" hooks: - id: editorconfig-checker alias: ec diff --git a/CHANGELOG.md b/CHANGELOG.md index 56e63438..27df403b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v0.0.1dev - [date] +## vdev - [date] Initial release of nf-core/circrna, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index 0103d545..fb3c1f6e 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,11 +12,11 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) -> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools diff --git a/LICENSE b/LICENSE index 8aa2385c..cbdceadb 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) Barry Digby, Nico Trummer +Copyright (c) Barry Digby Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index f5fc9571..558557f1 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/circrna/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/circrna/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -67,7 +67,8 @@ nextflow run nf-core/circrna \ ``` > [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; +> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/circrna/usage) and the [parameter documentation](https://nf-co.re/circrna/parameters). @@ -79,7 +80,7 @@ For more details about the output files and reports, please refer to the ## Credits -nf-core/circrna was originally written by Barry Digby, Nico Trummer. +nf-core/circrna was originally written by Barry Digby. We thank the following people for their extensive assistance in the development of this pipeline: diff --git a/assets/schema_input.json b/assets/schema_input.json index fd10663a..fe551cb8 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "https://json-schema.org/draft/2020-12/schema", + "$schema": "http://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/nf-core/circrna/master/assets/schema_input.json", "title": "nf-core/circrna pipeline - params.input schema", "description": "Schema for the file provided with params.input", diff --git a/conf/base.config b/conf/base.config index aaf44bfe..cdf46e83 100644 --- a/conf/base.config +++ b/conf/base.config @@ -11,9 +11,9 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { 1 * task.attempt } - memory = { 6.GB * task.attempt } - time = { 4.h * task.attempt } + cpus = { check_max( 1 * task.attempt, 'cpus' ) } + memory = { check_max( 6.GB * task.attempt, 'memory' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 @@ -27,30 +27,30 @@ process { // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { 1 } - memory = { 6.GB * task.attempt } - time = { 4.h * task.attempt } + cpus = { check_max( 1 , 'cpus' ) } + memory = { check_max( 6.GB * task.attempt, 'memory' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } } withLabel:process_low { - cpus = { 2 * task.attempt } - memory = { 12.GB * task.attempt } - time = { 4.h * task.attempt } + cpus = { check_max( 2 * task.attempt, 'cpus' ) } + memory = { check_max( 12.GB * task.attempt, 'memory' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } } withLabel:process_medium { - cpus = { 6 * task.attempt } - memory = { 36.GB * task.attempt } - time = { 8.h * task.attempt } + cpus = { check_max( 6 * task.attempt, 'cpus' ) } + memory = { check_max( 36.GB * task.attempt, 'memory' ) } + time = { check_max( 8.h * task.attempt, 'time' ) } } withLabel:process_high { - cpus = { 12 * task.attempt } - memory = { 72.GB * task.attempt } - time = { 16.h * task.attempt } + cpus = { check_max( 12 * task.attempt, 'cpus' ) } + memory = { check_max( 72.GB * task.attempt, 'memory' ) } + time = { check_max( 16.h * task.attempt, 'time' ) } } withLabel:process_long { - time = { 20.h * task.attempt } + time = { check_max( 20.h * task.attempt, 'time' ) } } withLabel:process_high_memory { - memory = { 200.GB * task.attempt } + memory = { check_max( 200.GB * task.attempt, 'memory' ) } } withLabel:error_ignore { errorStrategy = 'ignore' diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config deleted file mode 100644 index b4034d82..00000000 --- a/conf/igenomes_ignored.config +++ /dev/null @@ -1,9 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for iGenomes paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Empty genomes dictionary to use when igenomes is ignored. ----------------------------------------------------------------------------------------- -*/ - -params.genomes = [:] diff --git a/conf/modules.config b/conf/modules.config index d266a387..d203d2b6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -21,6 +21,7 @@ process { withName: FASTQC { ext.args = '--quiet' } + withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/test.config b/conf/test.config index 4c30298f..a7c2516f 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,18 +10,15 @@ ---------------------------------------------------------------------------------------- */ -process { - resourceLimits = [ - cpus: 4, - memory: '15.GB', - time: '1.h' - ] -} - params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' + // Limit resources so that this can run on GitHub Actions + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' + // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png new file mode 100755 index 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zXwhtT%ei{n#FzEH|C;yZ>+$!u_x#*+`=L8{b9SH^9&27u3G_Gxqxe`L2UJtdxghk z&-wzDFvLvW{chK5u3{n6GSKKy!P&C6w^IFpbD0bcp^A{{2lcLh_DXj@ybtYvc^;(2 M)78&qol`;+0Fu7JivR!s literal 0 HcmV?d00001 diff --git a/docs/output.md b/docs/output.md index 23814600..afc2a9d2 100644 --- a/docs/output.md +++ b/docs/output.md @@ -29,6 +29,16 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). +![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) + +![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) + +![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) + +:::note +The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. +::: + ### MultiQC
    diff --git a/docs/usage.md b/docs/usage.md index de4b1c3b..98e72a06 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -85,9 +85,9 @@ The above pipeline run specified with a params file in yaml format: nextflow run nf-core/circrna -profile docker -params-file params.yaml ``` -with: +with `params.yaml` containing: -```yaml title="params.yaml" +```yaml input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' @@ -199,6 +199,14 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). +## Azure Resource Requests + +To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. +We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. + +Note that the choice of VM size depends on your quota and the overall workload during the analysis. +For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). + ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/main.nf b/main.nf index 7b13c979..810b3959 100644 --- a/main.nf +++ b/main.nf @@ -9,6 +9,8 @@ ---------------------------------------------------------------------------------------- */ +nextflow.enable.dsl = 2 + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS @@ -18,6 +20,7 @@ include { CIRCRNA } from './workflows/circrna' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_circrna_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_circrna_pipeline' + include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_circrna_pipeline' /* @@ -53,8 +56,10 @@ workflow NFCORE_CIRCRNA { CIRCRNA ( samplesheet ) + emit: multiqc_report = CIRCRNA.out.multiqc_report // channel: /path/to/multiqc_report.html + } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -65,11 +70,13 @@ workflow NFCORE_CIRCRNA { workflow { main: + // // SUBWORKFLOW: Run initialisation tasks // PIPELINE_INITIALISATION ( params.version, + params.help, params.validate_params, params.monochrome_logs, args, @@ -83,6 +90,7 @@ workflow { NFCORE_CIRCRNA ( PIPELINE_INITIALISATION.out.samplesheet ) + // // SUBWORKFLOW: Run completion tasks // diff --git a/modules.json b/modules.json index d04c0809..3b1e37ee 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", + "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", + "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", "installed_by": ["subworkflows"] }, - "utils_nfschema_plugin": { + "utils_nfvalidation_plugin": { "branch": "master", - "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 691d4c76..1787b38a 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,5 +1,7 @@ +name: fastqc channels: - conda-forge - bioconda + - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d8989f48..d79f1c86 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -26,10 +26,7 @@ process FASTQC { def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) - // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 - // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4827da7a..ee5507e0 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,44 +16,35 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] - identifier: biotools:fastqc input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - html: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.html": - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.zip": - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index e9d79a07..70edae4d 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,14 +23,17 @@ nextflow_process { then { assertAll ( - { assert process.success }, - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
    Mon 2 Oct 2023
    test.gz
    - // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
    Mon 2 Oct 2023
    test.gz
    + // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_single") } ) } } @@ -51,14 +54,16 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_paired") } ) } } @@ -78,11 +83,13 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } ) } } @@ -102,11 +109,13 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_bam") } ) } } @@ -129,20 +138,22 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } ) } } @@ -162,116 +173,27 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } - ) - } - } + { assert process.success }, - test("sarscov2 single-end [fastq] - stub") { + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } ) } } - test("sarscov2 paired-end [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 interleaved [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 paired-end [bam] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } + test("sarscov2 single-end [fastq] - stub") { - test("sarscov2 multiple [fastq] - stub") { + options "-stub" - options "-stub" when { process { """ input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + [ id: 'test', single_end:true ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ]) """ } @@ -279,31 +201,12 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert process.success }, + { assert snapshot(process.out.html.collect { file(it[1]).getName() } + + process.out.zip.collect { file(it[1]).getName() } + + process.out.versions ).match("fastqc_stub") } ) } } - test("sarscov2 custom_prefix - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [ id:'mysample', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index d5db3092..86f7c311 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,392 +1,88 @@ { - "sarscov2 custom_prefix": { + "fastqc_versions_interleaved": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:16.374038" + "timestamp": "2024-01-31T17:40:07.293713" }, - "sarscov2 single-end [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": true - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": true - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:02:24.993809" - }, - "sarscov2 custom_prefix - stub": { - "content": [ - { - "0": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:03:10.93942" - }, - "sarscov2 interleaved [fastq]": { + "fastqc_stub": { "content": [ [ + "test.html", + "test.zip", "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:01:42.355718" + "timestamp": "2024-01-31T17:31:01.425198" }, - "sarscov2 paired-end [bam]": { + "fastqc_versions_multiple": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:01:53.276274" + "timestamp": "2024-01-31T17:40:55.797907" }, - "sarscov2 multiple [fastq]": { + "fastqc_versions_bam": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:05.527626" + "timestamp": "2024-01-31T17:40:26.795862" }, - "sarscov2 paired-end [fastq]": { + "fastqc_versions_single": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:01:31.188871" - }, - "sarscov2 paired-end [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:34.273566" + "timestamp": "2024-01-31T17:39:27.043675" }, - "sarscov2 multiple [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:03:02.304411" - }, - "sarscov2 single-end [fastq]": { + "fastqc_versions_paired": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:01:19.095607" - }, - "sarscov2 interleaved [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:44.640184" + "timestamp": "2024-01-31T17:39:47.584191" }, - "sarscov2 paired-end [bam] - stub": { + "fastqc_versions_custom_prefix": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:53.550742" + "timestamp": "2024-01-31T17:41:14.576531" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 6f5b867b..ca39fb67 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,5 +1,7 @@ +name: multiqc channels: - conda-forge - bioconda + - defaults dependencies: - - bioconda::multiqc=1.25.1 + - bioconda::multiqc=1.21 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index cc0643e1..47ac352f 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,16 +3,14 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : + 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) - path(replace_names) - path(sample_names) output: path "*multiqc_report.html", emit: report @@ -25,22 +23,16 @@ process MULTIQC { script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' - def replace = replace_names ? "--replace-names ${replace_names}" : '' - def samples = sample_names ? "--sample-names ${sample_names}" : '' + def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' """ multiqc \\ --force \\ $args \\ $config \\ - $prefix \\ $extra_config \\ $logo \\ - $replace \\ - $samples \\ . cat <<-END_VERSIONS > versions.yml @@ -52,7 +44,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - mkdir multiqc_plots + touch multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index b16c1879..45a9bc35 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,6 +1,5 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into - a single report +description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC - bioinformatics tools @@ -13,59 +12,40 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - identifier: biotools:multiqc input: - - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections - in multiqc_config. - pattern: "*.{yml,yaml}" - - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - - - replace_names: - type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - - - sample_names: - type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. + pattern: "*.{yml,yaml}" + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" output: - report: - - "*multiqc_report.html": - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - - "*_data": - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - - "*_plots": - type: file - description: Plots created by MultiQC - pattern: "*_data" + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 33316a7d..f1c4242e 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,8 +8,6 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" - config "./nextflow.config" - test("sarscov2 single-end [fastqc]") { when { @@ -19,8 +17,6 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] - input[4] = [] - input[5] = [] """ } } @@ -45,8 +41,6 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] - input[4] = [] - input[5] = [] """ } } @@ -72,8 +66,6 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] - input[4] = [] - input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 2fcbb5ff..bfebd802 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-10-02T17:51:46.317523" + "timestamp": "2024-02-29T08:48:55.657331" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-10-02T17:52:20.680978" + "timestamp": "2024-02-29T08:49:49.071937" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-10-02T17:52:09.185842" + "timestamp": "2024-02-29T08:49:25.457567" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config deleted file mode 100644 index c537a6a3..00000000 --- a/modules/nf-core/multiqc/tests/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: 'MULTIQC' { - ext.prefix = null - } -} diff --git a/nextflow.config b/nextflow.config index 7f032f1e..13ad97ff 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,7 +12,6 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null - // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' @@ -34,27 +33,48 @@ params { monochrome_logs = false hook_url = null help = false - help_full = false - show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' // Config options config_profile_name = null config_profile_description = null - custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null + // Max resource options + // Defaults only, expecting to be overwritten + max_memory = '128.GB' + max_cpus = 16 + max_time = '240.h' + // Schema validation default options - validate_params = true + validationFailUnrecognisedParams = false + validationLenientMode = false + validationSchemaIgnoreParams = 'genomes,igenomes_base' + validationShowHiddenParams = false + validate_params = true + } // Load base.config by default for all pipelines includeConfig 'conf/base.config' +// Load nf-core custom profiles from different Institutions +try { + includeConfig "${params.custom_config_base}/nfcore_custom.config" +} catch (Exception e) { + System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") +} + +// Load nf-core/circrna custom profiles from different institutions. +try { + includeConfig "${params.custom_config_base}/pipeline/circrna.config" +} catch (Exception e) { + System.err.println("WARNING: Could not load nf-core/config/circrna profiles: ${params.custom_config_base}/pipeline/circrna.config") +} profiles { debug { dumpHashes = true @@ -69,7 +89,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda'] + conda.channels = ['conda-forge', 'bioconda', 'defaults'] apptainer.enabled = false } mamba { @@ -158,25 +178,25 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } -// Load nf-core custom profiles from different Institutions -includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" - -// Load nf-core/circrna custom profiles from different institutions. -// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs -// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/circrna.config" : "/dev/null" - -// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled +// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled // Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' -charliecloud.registry = 'quay.io' +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' -// Load igenomes.config if required -includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' +// Nextflow plugins +plugins { + id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} +// Load igenomes.config if required +if (!params.igenomes_ignore) { + includeConfig 'conf/igenomes.config' +} else { + params.genomes = [:] +} // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -188,15 +208,8 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Set bash options -process.shell = """\ -bash - -set -e # Exit if a tool returns a non-zero status/exit code -set -u # Treat unset variables and parameters as an error -set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute -set -C # No clobber - prevent output redirection from overwriting files. -""" +// Capture exit codes from upstream processes when piping +process.shell = ['/bin/bash', '-euo', 'pipefail'] // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false @@ -221,50 +234,47 @@ dag { manifest { name = 'nf-core/circrna' - author = """Barry Digby, Nico Trummer""" + author = """Barry Digby""" homePage = 'https://github.com/nf-core/circrna' description = """Quantification, miRNA target prediction and differential expression analysis of circular RNAs""" mainScript = 'main.nf' - nextflowVersion = '!>=24.04.2' - version = '0.0.1dev' + nextflowVersion = '!>=23.04.0' + version = 'dev' doi = '' } -// Nextflow plugins -plugins { - id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} - -validation { - defaultIgnoreParams = ["genomes"] - help { - enabled = true - command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " - fullParameter = "help_full" - showHiddenParameter = "show_hidden" - beforeText = """ --\033[2m----------------------------------------------------\033[0m- - \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m -\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m -\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m -\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m - \033[0;32m`._,._,\'\033[0m -\033[0;35m ${manifest.name} ${manifest.version}\033[0m --\033[2m----------------------------------------------------\033[0m- -""" - afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} -* The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' -* Software dependencies - https://github.com/${manifest.name}/blob/master/CITATIONS.md -""" - } - summary { - beforeText = validation.help.beforeText - afterText = validation.help.afterText +// Function to ensure that resource requirements don't go beyond +// a maximum limit +def check_max(obj, type) { + if (type == 'memory') { + try { + if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) + return params.max_memory as nextflow.util.MemoryUnit + else + return obj + } catch (all) { + println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" + return obj + } + } else if (type == 'time') { + try { + if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) + return params.max_time as nextflow.util.Duration + else + return obj + } catch (all) { + println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" + return obj + } + } else if (type == 'cpus') { + try { + return Math.min( obj, params.max_cpus as int ) + } catch (all) { + println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" + return obj + } } } - -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index b24ff3db..82858e99 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "https://json-schema.org/draft/2020-12/schema", + "$schema": "http://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/nf-core/circrna/master/nextflow_schema.json", "title": "nf-core/circrna pipeline parameters", "description": "Quantification, miRNA target prediction and differential expression analysis of circular RNAs", "type": "object", - "$defs": { + "definitions": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -71,14 +71,6 @@ "fa_icon": "fas fa-ban", "hidden": true, "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." - }, - "igenomes_base": { - "type": "string", - "format": "directory-path", - "description": "The base path to the igenomes reference files", - "fa_icon": "fas fa-ban", - "hidden": true, - "default": "s3://ngi-igenomes/igenomes/" } } }, @@ -130,6 +122,41 @@ } } }, + "max_job_request_options": { + "title": "Max job request options", + "type": "object", + "fa_icon": "fab fa-acquisitions-incorporated", + "description": "Set the top limit for requested resources for any single job.", + "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", + "properties": { + "max_cpus": { + "type": "integer", + "description": "Maximum number of CPUs that can be requested for any single job.", + "default": 16, + "fa_icon": "fas fa-microchip", + "hidden": true, + "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" + }, + "max_memory": { + "type": "string", + "description": "Maximum amount of memory that can be requested for any single job.", + "default": "128.GB", + "fa_icon": "fas fa-memory", + "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", + "hidden": true, + "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" + }, + "max_time": { + "type": "string", + "description": "Maximum amount of time that can be requested for any single job.", + "default": "240.h", + "fa_icon": "far fa-clock", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", + "hidden": true, + "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" + } + } + }, "generic_options": { "title": "Generic options", "type": "object", @@ -137,6 +164,12 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { + "help": { + "type": "boolean", + "description": "Display help text.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -212,6 +245,27 @@ "fa_icon": "fas fa-check-square", "hidden": true }, + "validationShowHiddenParams": { + "type": "boolean", + "fa_icon": "far fa-eye-slash", + "description": "Show all params when using `--help`", + "hidden": true, + "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." + }, + "validationFailUnrecognisedParams": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters fails when an unrecognised parameter is found.", + "hidden": true, + "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." + }, + "validationLenientMode": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters in lenient more.", + "hidden": true, + "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." + }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", @@ -224,16 +278,19 @@ }, "allOf": [ { - "$ref": "#/$defs/input_output_options" + "$ref": "#/definitions/input_output_options" + }, + { + "$ref": "#/definitions/reference_genome_options" }, { - "$ref": "#/$defs/reference_genome_options" + "$ref": "#/definitions/institutional_config_options" }, { - "$ref": "#/$defs/institutional_config_options" + "$ref": "#/definitions/max_job_request_options" }, { - "$ref": "#/$defs/generic_options" + "$ref": "#/definitions/generic_options" } ] } diff --git a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf index aae83125..5ee14910 100644 --- a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf @@ -8,25 +8,29 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { samplesheetToList } from 'plugin/nf-schema' +include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { fromSamplesheet } from 'plugin/nf-validation' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' +include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' +include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== SUBWORKFLOW TO INITIALISE PIPELINE -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit + help // boolean: Display help text validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args @@ -50,10 +54,16 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // - UTILS_NFSCHEMA_PLUGIN ( - workflow, + pre_help_text = nfCoreLogo(monochrome_logs) + post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) + def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " + UTILS_NFVALIDATION_PLUGIN ( + help, + workflow_command, + pre_help_text, + post_help_text, validate_params, - null + "nextflow_schema.json" ) // @@ -62,7 +72,6 @@ workflow PIPELINE_INITIALISATION { UTILS_NFCORE_PIPELINE ( nextflow_cli_args ) - // // Custom validation for pipeline parameters // @@ -71,9 +80,8 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // - Channel - .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) + .fromSamplesheet("input") .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -83,8 +91,8 @@ workflow PIPELINE_INITIALISATION { } } .groupTuple() - .map { samplesheet -> - validateInputSamplesheet(samplesheet) + .map { + validateInputSamplesheet(it) } .map { meta, fastqs -> @@ -98,9 +106,9 @@ workflow PIPELINE_INITIALISATION { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== SUBWORKFLOW FOR PIPELINE COMPLETION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ workflow PIPELINE_COMPLETION { @@ -115,6 +123,7 @@ workflow PIPELINE_COMPLETION { multiqc_report // string: Path to MultiQC report main: + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") // @@ -122,18 +131,11 @@ workflow PIPELINE_COMPLETION { // workflow.onComplete { if (email || email_on_fail) { - completionEmail( - summary_params, - email, - email_on_fail, - plaintext_email, - outdir, - monochrome_logs, - multiqc_report.toList() - ) + completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) } completionSummary(monochrome_logs) + if (hook_url) { imNotification(summary_params, hook_url) } @@ -145,9 +147,9 @@ workflow PIPELINE_COMPLETION { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ // // Check and validate pipeline parameters @@ -163,7 +165,7 @@ def validateInputSamplesheet(input) { def (metas, fastqs) = input[1..2] // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 + def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 if (!endedness_ok) { error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") } @@ -195,6 +197,7 @@ def genomeExistsError() { error(error_string) } } + // // Generate methods description for MultiQC // @@ -236,10 +239,8 @@ def methodsDescriptionText(mqc_methods_yaml) { // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list def temp_doi_ref = "" - def manifest_doi = meta.manifest_map.doi.tokenize(",") - manifest_doi.each { doi_ref -> - temp_doi_ref += "(doi:     ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " - } + String[] manifest_doi = meta.manifest_map.doi.tokenize(",") + for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) } else meta["doi_text"] = "" meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " @@ -260,4 +261,3 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } - diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 0fcbf7b3..ac31f28f 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,13 +2,18 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // +import org.yaml.snakeyaml.Yaml +import groovy.json.JsonOutput +import nextflow.extension.FilesEx + /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ workflow UTILS_NEXTFLOW_PIPELINE { + take: print_version // boolean: print version dump_parameters // boolean: dump parameters @@ -21,7 +26,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Print workflow version and exit on --version // if (print_version) { - log.info("${workflow.manifest.name} ${getWorkflowVersion()}") + log.info "${workflow.manifest.name} ${getWorkflowVersion()}" System.exit(0) } @@ -44,16 +49,16 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ // // Generate version string // def getWorkflowVersion() { - def version_string = "" as String + String version_string = "" if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -71,13 +76,13 @@ def getWorkflowVersion() { // Dump pipeline parameters to a JSON file // def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = groovy.json.JsonOutput.toJson(params) - temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) + def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = JsonOutput.toJson(params) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) - nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() } @@ -85,40 +90,37 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - def parser = new org.yaml.snakeyaml.Yaml() + Yaml parser = new Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) channels = config.channels - } - catch (NullPointerException e) { - log.warn("Could not verify conda channel configuration.") - return null - } - catch (IOException e) { - log.warn("Could not verify conda channel configuration.") - return null + } catch(NullPointerException | IOException e) { + log.warn "Could not verify conda channel configuration." + return } // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda'] + def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } + def channel_priority_violation = false + def n = required_channels_in_order.size() + for (int i = 0; i < n - 1; i++) { + channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + } if (channels_missing | channel_priority_violation) { - log.warn """\ - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - There is a problem with your Conda configuration! - You will need to set-up the conda-forge and bioconda channels correctly. - Please refer to https://bioconda.github.io/ - The observed channel order is - ${channels} - but the following channel order is required: - ${required_channels_in_order} - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - """.stripIndent(true) + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " There is a problem with your Conda configuration!\n\n" + + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + + " Please refer to https://bioconda.github.io/\n" + + " The observed channel order is \n" + + " ${channels}\n" + + " but the following channel order is required:\n" + + " ${required_channels_in_order}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index a09572e5..d0a926bf 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 5cb7bafe..14558c39 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,13 +2,17 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // +import org.yaml.snakeyaml.Yaml +import nextflow.extension.FilesEx + /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ workflow UTILS_NFCORE_PIPELINE { + take: nextflow_cli_args @@ -21,20 +25,23 @@ workflow UTILS_NFCORE_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ // // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - def valid_config = true as Boolean + valid_config = true if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn( - "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " - ) + log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + + "Please refer to the quick start section and usage docs for the pipeline.\n " valid_config = false } return valid_config @@ -45,14 +52,12 @@ def checkConfigProvided() { // def checkProfileProvided(nextflow_cli_args) { if (workflow.profile.endsWith(',')) { - error( - "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" - ) + error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" } if (nextflow_cli_args[0]) { - log.warn( - "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" - ) + log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" } } @@ -61,21 +66,25 @@ def checkProfileProvided(nextflow_cli_args) { // def workflowCitation() { def temp_doi_ref = "" - def manifest_doi = workflow.manifest.doi.tokenize(",") - // Handling multiple DOIs + String[] manifest_doi = workflow.manifest.doi.tokenize(",") + // Using a loop to handle multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list - manifest_doi.each { doi_ref -> - temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" - } - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" + for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + "* The pipeline\n" + + temp_doi_ref + "\n" + + "* The nf-core framework\n" + + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + + "* Software dependencies\n" + + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } // // Generate workflow version string // def getWorkflowVersion() { - def version_string = "" as String + String version_string = "" if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -93,8 +102,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - def yaml = new org.yaml.snakeyaml.Yaml() - def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } + Yaml yaml = new Yaml() + versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } return yaml.dumpAsMap(versions).trim() } @@ -104,8 +113,8 @@ def processVersionsFromYAML(yaml_file) { def workflowVersionToYAML() { return """ Workflow: - ${workflow.manifest.name}: ${getWorkflowVersion()} - Nextflow: ${workflow.nextflow.version} + $workflow.manifest.name: ${getWorkflowVersion()} + Nextflow: $workflow.nextflow.version """.stripIndent().trim() } @@ -113,7 +122,11 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) + return ch_versions + .unique() + .map { processVersionsFromYAML(it) } + .unique() + .mix(Channel.of(workflowVersionToYAML())) } // @@ -121,31 +134,25 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - summary_params - .keySet() - .each { group -> - def group_params = summary_params.get(group) - // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    ${group}

    \n" - summary_section += "
    \n" - group_params - .keySet() - .sort() - .each { param -> - summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" - } - summary_section += "
    \n" + for (group in summary_params.keySet()) { + def group_params = summary_params.get(group) // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    $group

    \n" + summary_section += "
    \n" + for (param in group_params.keySet()) { + summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" } + summary_section += "
    \n" } + } - def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" return yaml_file_text } @@ -154,7 +161,7 @@ def paramsSummaryMultiqc(summary_params) { // nf-core logo // def nfCoreLogo(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map + Map colors = logColours(monochrome_logs) String.format( """\n ${dashedLine(monochrome_logs)} @@ -173,7 +180,7 @@ def nfCoreLogo(monochrome_logs=true) { // Return dashed line // def dashedLine(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map + Map colors = logColours(monochrome_logs) return "-${colors.dim}----------------------------------------------------${colors.reset}-" } @@ -181,7 +188,7 @@ def dashedLine(monochrome_logs=true) { // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - def colorcodes = [:] as Map + Map colorcodes = [:] // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -193,54 +200,54 @@ def logColours(monochrome_logs=true) { colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" return colorcodes } @@ -255,15 +262,14 @@ def attachMultiqcReport(multiqc_report) { mqc_report = multiqc_report.getVal() if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { if (mqc_report.size() > 1) { - log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") + log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" } mqc_report = mqc_report[0] } } - } - catch (Exception all) { + } catch (all) { if (multiqc_report) { - log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") + log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" } } return mqc_report @@ -275,35 +281,26 @@ def attachMultiqcReport(multiqc_report) { def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { // Set up the e-mail variables - def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" + def subject = "[$workflow.manifest.name] Successful: $workflow.runName" if (!workflow.success) { - subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" + subject = "[$workflow.manifest.name] FAILED: $workflow.runName" } def summary = [:] - summary_params - .keySet() - .sort() - .each { group -> - summary << summary_params[group] - } + for (group in summary_params.keySet()) { + summary << summary_params[group] + } def misc_fields = [:] misc_fields['Date Started'] = workflow.start misc_fields['Date Completed'] = workflow.complete misc_fields['Pipeline script file path'] = workflow.scriptFile misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) { - misc_fields['Pipeline repository Git URL'] = workflow.repository - } - if (workflow.commitId) { - misc_fields['Pipeline repository Git Commit'] = workflow.commitId - } - if (workflow.revision) { - misc_fields['Pipeline Git branch/tag'] = workflow.revision - } - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build + if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository + if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId + if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] @@ -341,41 +338,39 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Render the sendmail template def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] + def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - def colors = logColours(monochrome_logs) as Map + Map colors = logColours(monochrome_logs) if (email_address) { try { - if (plaintext_email) { -new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } - ['sendmail', '-t'].execute() << sendmail_html - log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") - } - catch (Exception all) { + [ 'sendmail', '-t' ].execute() << sendmail_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" + } catch (all) { // Catch failures and try with plaintext - def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] + def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] mail_cmd.execute() << email_html - log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" } } // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") + FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") + FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); output_tf.delete() } @@ -383,17 +378,15 @@ new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map + Map colors = logColours(monochrome_logs) if (workflow.success) { if (workflow.stats.ignoredCount == 0) { - log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") - } - else { - log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" } - } - else { - log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" } } @@ -402,30 +395,21 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - summary_params - .keySet() - .sort() - .each { group -> - summary << summary_params[group] - } + for (group in summary_params.keySet()) { + summary << summary_params[group] + } def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) { - misc_fields['repository'] = workflow.repository - } - if (workflow.commitId) { - misc_fields['commitid'] = workflow.commitId - } - if (workflow.revision) { - misc_fields['revision'] = workflow.revision - } - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) misc_fields['repository'] = workflow.repository + if (workflow.commitId) misc_fields['commitid'] = workflow.commitId + if (workflow.revision) misc_fields['revision'] = workflow.revision + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp def msg_fields = [:] msg_fields['version'] = getWorkflowVersion() @@ -450,13 +434,13 @@ def imNotification(summary_params, hook_url) { def json_message = json_template.toString() // POST - def post = new URL(hook_url).openConnection() + def post = new URL(hook_url).openConnection(); post.setRequestMethod("POST") post.setDoOutput(true) post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")) - def postRC = post.getResponseCode() - if (!postRC.equals(200)) { - log.warn(post.getErrorStream().getText()) + post.getOutputStream().write(json_message.getBytes("UTF-8")); + def postRC = post.getResponseCode(); + if (! postRC.equals(200)) { + log.warn(post.getErrorStream().getText()); } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf deleted file mode 100644 index 4994303e..00000000 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ /dev/null @@ -1,46 +0,0 @@ -// -// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary -// - -include { paramsSummaryLog } from 'plugin/nf-schema' -include { validateParameters } from 'plugin/nf-schema' - -workflow UTILS_NFSCHEMA_PLUGIN { - - take: - input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow - validate_params // boolean: validate the parameters - parameters_schema // string: path to the parameters JSON schema. - // this has to be the same as the schema given to `validation.parametersSchema` - // when this input is empty it will automatically use the configured schema or - // "${projectDir}/nextflow_schema.json" as default. This input should not be empty - // for meta pipelines - - main: - - // - // Print parameter summary to stdout. This will display the parameters - // that differ from the default given in the JSON schema - // - if(parameters_schema) { - log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) - } else { - log.info paramsSummaryLog(input_workflow) - } - - // - // Validate the parameters using nextflow_schema.json or the schema - // given via the validation.parametersSchema configuration option - // - if(validate_params) { - if(parameters_schema) { - validateParameters(parameters_schema:parameters_schema) - } else { - validateParameters() - } - } - - emit: - dummy_emit = true -} - diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml deleted file mode 100644 index f7d9f028..00000000 --- a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml +++ /dev/null @@ -1,35 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "utils_nfschema_plugin" -description: Run nf-schema to validate parameters and create a summary of changed parameters -keywords: - - validation - - JSON schema - - plugin - - parameters - - summary -components: [] -input: - - input_workflow: - type: object - description: | - The workflow object of the used pipeline. - This object contains meta data used to create the params summary log - - validate_params: - type: boolean - description: Validate the parameters and error if invalid. - - parameters_schema: - type: string - description: | - Path to the parameters JSON schema. - This has to be the same as the schema given to the `validation.parametersSchema` config - option. When this input is empty it will automatically use the configured schema or - "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way - for meta pipelines. -output: - - dummy_emit: - type: boolean - description: Dummy emit to make nf-core subworkflows lint happy -authors: - - "@nvnieuwk" -maintainers: - - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test deleted file mode 100644 index 842dc432..00000000 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ /dev/null @@ -1,117 +0,0 @@ -nextflow_workflow { - - name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" - script "../main.nf" - workflow "UTILS_NFSCHEMA_PLUGIN" - - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/utils_nfschema_plugin" - tag "plugin/nf-schema" - - config "./nextflow.config" - - test("Should run nothing") { - - when { - - params { - test_data = '' - } - - workflow { - """ - validate_params = false - input[0] = workflow - input[1] = validate_params - input[2] = "" - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should validate params") { - - when { - - params { - test_data = '' - outdir = 1 - } - - workflow { - """ - validate_params = true - input[0] = workflow - input[1] = validate_params - input[2] = "" - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } - ) - } - } - - test("Should run nothing - custom schema") { - - when { - - params { - test_data = '' - } - - workflow { - """ - validate_params = false - input[0] = workflow - input[1] = validate_params - input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should validate params - custom schema") { - - when { - - params { - test_data = '' - outdir = 1 - } - - workflow { - """ - validate_params = true - input[0] = workflow - input[1] = validate_params - input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config deleted file mode 100644 index 0907ac58..00000000 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -plugins { - id "nf-schema@2.1.0" -} - -validation { - parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" - monochromeLogs = true -} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf new file mode 100644 index 00000000..2585b65d --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf @@ -0,0 +1,62 @@ +// +// Subworkflow that uses the nf-validation plugin to render help text and parameter summary +// + +/* +======================================================================================== + IMPORT NF-VALIDATION PLUGIN +======================================================================================== +*/ + +include { paramsHelp } from 'plugin/nf-validation' +include { paramsSummaryLog } from 'plugin/nf-validation' +include { validateParameters } from 'plugin/nf-validation' + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFVALIDATION_PLUGIN { + + take: + print_help // boolean: print help + workflow_command // string: default commmand used to run pipeline + pre_help_text // string: string to be printed before help text and summary log + post_help_text // string: string to be printed after help text and summary log + validate_params // boolean: validate parameters + schema_filename // path: JSON schema file, null to use default value + + main: + + log.debug "Using schema file: ${schema_filename}" + + // Default values for strings + pre_help_text = pre_help_text ?: '' + post_help_text = post_help_text ?: '' + workflow_command = workflow_command ?: '' + + // + // Print help message if needed + // + if (print_help) { + log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text + System.exit(0) + } + + // + // Print parameter summary to stdout + // + log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text + + // + // Validate parameters relative to the parameter JSON schema + // + if (validate_params){ + validateParameters(parameters_schema: schema_filename) + } + + emit: + dummy_emit = true +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml new file mode 100644 index 00000000..3d4a6b04 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml @@ -0,0 +1,44 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFVALIDATION_PLUGIN" +description: Use nf-validation to initiate and validate a pipeline +keywords: + - utility + - pipeline + - initialise + - validation +components: [] +input: + - print_help: + type: boolean + description: | + Print help message and exit + - workflow_command: + type: string + description: | + The command to run the workflow e.g. "nextflow run main.nf" + - pre_help_text: + type: string + description: | + Text to print before the help message + - post_help_text: + type: string + description: | + Text to print after the help message + - validate_params: + type: boolean + description: | + Validate the parameters and error if invalid. + - schema_filename: + type: string + description: | + The filename of the schema to validate against. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test new file mode 100644 index 00000000..5784a33f --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -0,0 +1,200 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFVALIDATION_PLUGIN" + script "../main.nf" + workflow "UTILS_NFVALIDATION_PLUGIN" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "plugin/nf-validation" + tag "'plugin/nf-validation'" + tag "utils_nfvalidation_plugin" + tag "subworkflows/utils_nfvalidation_plugin" + + test("Should run nothing") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should run help") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with command") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with extra text") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = "pre-help-text" + post_help_text = "post-help-text" + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('pre-help-text') } }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } }, + { assert workflow.stdout.any { it.contains('post-help-text') } } + ) + } + } + + test("Should validate params") { + + when { + + params { + monochrome_logs = true + test_data = '' + outdir = 1 + } + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = true + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json similarity index 95% rename from subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json rename to subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json index 331e0d2f..7626c1c9 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "https://json-schema.org/draft/2020-12/schema", + "$schema": "http://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "$defs": { + "definitions": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/$defs/input_output_options" + "$ref": "#/definitions/input_output_options" }, { - "$ref": "#/$defs/generic_options" + "$ref": "#/definitions/generic_options" } ] } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml new file mode 100644 index 00000000..60b1cfff --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfvalidation_plugin: + - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 1f63f055..da558a8e 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -3,9 +3,10 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ + include { FASTQC } from '../modules/nf-core/fastqc/main' include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-schema' +include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_circrna_pipeline' @@ -20,10 +21,12 @@ workflow CIRCRNA { take: ch_samplesheet // channel: samplesheet read in from --input + main: ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() + // // MODULE: Run FastQC // @@ -39,12 +42,11 @@ workflow CIRCRNA { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml', + name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true ).set { ch_collated_versions } - // // MODULE: MultiQC // @@ -60,14 +62,15 @@ workflow CIRCRNA { summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) ch_methods_description = Channel.value( methodsDescriptionText(ch_multiqc_custom_methods_description)) + ch_multiqc_files = ch_multiqc_files.mix( + ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) ch_multiqc_files = ch_multiqc_files.mix( ch_methods_description.collectFile( @@ -80,14 +83,12 @@ workflow CIRCRNA { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList(), - [], - [] + ch_multiqc_logo.toList() ) - emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + emit: + multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] - } /*