conda-free and nf-test

.gitignore

@@ -11,3 +11,8 @@ testing*
 venv/
 params*.json
 sample_manifest*
+*.log
+tests/sample-data/*
+tests/ref/*
+!**/.gitkeep
+.nf-test/

CHANGELOG.md

@@ -55,4 +55,9 @@ Initial release of QUANTS, created with the [nf-core](https://nf-co.re/) templat
     * Ability to extract top 50 library-independent counts as FASTA
 ## 3.0.0.3 - [24th January 2024]
 
-* Hotfix to force COLLATE_CUTADAPT_JSONS to run on 1 cpu
+* Hotfix to force COLLATE_CUTADAPT_JSONS to run on 1 cpu
+
+## 3.0.0.4 - [7th November 2024]
+
+* Replace containers which use licensed conda packages
+* Remove galaxy depot

modules.json

@@ -7,14 +7,14 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d",
+                        "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164",
                         "installed_by": [
                             "modules"
                         ]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": [
                             "modules"
                         ]
@@ -23,4 +23,4 @@
             }
         }
     }
-}
+}

modules/local/cutadapt/main.nf

@@ -12,11 +12,8 @@ process CUTADAPT {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::cutadapt=4.4' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/cutadapt:4.4--py39hf95cd2a_1'
-    } else {
-        container 'quay.io/biocontainers/cutadapt:4.4--py39hf95cd2a_1'
-    }
+    container 'quay.io/biocontainers/cutadapt:4.4--py39hf95cd2a_1'
+
 
     input:
     tuple val(meta), path(reads)

modules/local/flash2/main.nf

@@ -11,11 +11,7 @@ process FLASH2 {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? "bioconda::flash=2.2.00" : null)
 
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/flash2:2.2.00--h5bf99c6_3"
-    } else {
-        container "quay.io/biocontainers/flash2:2.2.00--h5bf99c6_3"
-    }
+    container "quay.io/biocontainers/flash2:2.2.00--h5bf99c6_3"
 
     input:
     tuple val(meta), path(reads)

modules/local/get_software_versions.nf

@@ -9,11 +9,7 @@ process GET_SOFTWARE_VERSIONS {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
-    } else {
-        container "quay.io/biocontainers/python:3.8.3"
-    }
+    container "quay.io/biocontainers/python:3.8.3"
 
     cache false
 

modules/local/pyquest/main.nf

@@ -12,11 +12,7 @@ process PYQUEST {
 
     // Keep for when container is public
     /*
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/flash2:2.2.00--h5bf99c6_3"
-    } else {
-        container "quay.io/biocontainers/flash2:2.2.00--h5bf99c6_3"
-    }
+    container "quay.io/biocontainers/flash2:2.2.00--h5bf99c6_3"
     */
     container "quay.io/wtsicgp/pyquest:1.1.0"
 

modules/local/pyquest_library_converter/main.nf

@@ -10,12 +10,8 @@ process TRANSFORM_LIBRARY_FOR_PYQUEST {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pyquest', meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? null : null)
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
-    } else {
-        container "quay.io/biocontainers/python:3.8.3"
-    }
+    conda (params.enable_conda ? "conda-forge::python=3.12.7" : null)
+    container "docker.io/python:3.12.7"
 
     input:
         path(oligo_library)

modules/local/read_modification/main.nf

@@ -20,17 +20,27 @@ process APPEND_STRINGS_TO_FQ {
 
     script:
     def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def input = reads
     def append_start = params.append_start ? params.append_start : ""
     def append_end = params.append_end ? params.append_end : ""
     def append_quality_start = params.append_start ? params.append_quality*append_start.length() : ""
     def append_quality_end = params.append_end ? params.append_quality*append_end.length() : ""
     def output = "${prefix}.modified.fq.gz"
+    """
+    zcat ${input} | awk -v append_start="${append_start}" -v append_end="${append_end}" -v append_quality_start="${append_quality_start}" -v append_quality_end="${append_quality_end}" '
+        NR % 4 == 2 { print append_start \$0 append_end; next }
+        NR % 4 == 0 { print append_quality_start \$0 append_quality_end; next }
+        { print \$0 }
+        ' | gzip > ${output}
+    """
 
-    $/
-        zcat ${input} | \
-        sed -e '2~4s/^\(.*\)$/${append_start}\1${append_end}/' -e '4~4s/^\(.*\)$/${append_quality_start}\1${append_quality_end}/' | \
-        gzip > ${output}
-    /$
+
+    // "zcat ${input} | sed -e '2~4s/^\(.*\)$/${append_start}\1${append_end}/' -e '4~4s/^\(.*\)$/${append_quality_start}\1${append_quality_end}/' | gzip > ${output}'
+
+    // $/
+    //     zcat ${input} | \
+    //     sed -e '2~4s/^\(.*\)$/${append_start}\1${append_end}/' -e '4~4s/^\(.*\)$/${append_quality_start}\1${append_quality_end}/' | \
+    //     gzip > ${output}
+    // /$
 }

modules/local/samplesheet_check.nf

@@ -10,11 +10,7 @@ process SAMPLESHEET_CHECK_FASTQ {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
-    } else {
-        container "quay.io/biocontainers/python:3.8.3"
-    }
+    container "quay.io/biocontainers/python:3.8.3"
 
     input:
     path samplesheet
@@ -37,11 +33,7 @@ process SAMPLESHEET_CHECK_CRAM {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
-    } else {
-        container "quay.io/biocontainers/python:3.8.3"
-    }
+    container "quay.io/biocontainers/python:3.8.3"
 
     input:
     path samplesheet

modules/local/samtools/bam2fq/main.nf

@@ -3,9 +3,7 @@ process SAMTOOLS_BAM2FQ {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+    container 'quay.io/biocontainers/samtools:1.15--h1170115_1'
 
     input:
     tuple val(meta), path(inputbam)

modules/local/seqkit_seq/main.nf

@@ -13,12 +13,7 @@ process SEQKIT_SEQ {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process)+'_seq', meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::seqkit=0.15.0" : null)
-
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqkit:0.15.0--0"
-    } else {
-        container "quay.io/biocontainers/seqkit:0.15.0--0"
-    }
+    container "quay.io/biocontainers/seqkit:0.15.0--0"
 
     input:
         tuple val(meta), path(reads)

modules/local/seqkit_stats/main.nf

@@ -13,12 +13,7 @@ process SEQKIT_STATS {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process)+'_stats', meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::seqkit=0.15.0" : null)
-
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqkit:0.15.0--0"
-    } else {
-        container "quay.io/biocontainers/seqkit:0.15.0--0"
-    }
+    container "quay.io/biocontainers/seqkit:0.15.0--0"
 
     input:
         tuple val(meta), path(reads)

modules/local/seqprep/adapter_trimming/main.nf

@@ -11,11 +11,7 @@ process SEQPREP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? "bioconda::seqprep=1.3.2" : null)
 
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqprep:1.3.2--h5bf99c6_5"
-    } else {
-        container "quay.io/biocontainers/seqprep:1.3.2--h5bf99c6_5"
-    }
+    container "quay.io/biocontainers/seqprep:1.3.2--h5bf99c6_5"
 
     input:
     tuple val(meta), path(reads)

modules/local/seqprep/read_merging/main.nf

@@ -11,11 +11,7 @@ process SEQPREP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? "bioconda::seqprep=1.3.2" : null)
 
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqprep:1.3.2--h5bf99c6_5"
-    } else {
-        container "quay.io/biocontainers/seqprep:1.3.2--h5bf99c6_5"
-    }
+    container "quay.io/biocontainers/seqprep:1.3.2--h5bf99c6_5"
 
     input:
     tuple val(meta), path(reads)