Merge branch 'master' into islandpath

* master:
  Ngscheckmate (nf-core#3094)
  New module Mindagap (nf-core#2860)
  Coreograph Module (nf-core#3201)
  new module wisecondorx/newref (nf-core#3212)
  Add core detection test data to config (nf-core#3199)
  Collectinsertsizemetrics (nf-core#3179)
  update appropriate label for freyja boot (nf-core#3215)
  Emit files from uncompression utilities (nf-core#3144)
  new tool: art_illumina (nf-core#3162)
  Addition of new module: Issue nf-core#3113 Survivor/filter (nf-core#3168)
  Removed -1 in CPU size specification for samtools in BWA module (nf-core#3205)
  nf-test Transition CI (nf-core#3191)
  new module: sourmash/index (nf-core#3163)
  Chopper (nf-core#3174)
  Update mapdage2 module (nf-core#3185)
  Add imaging test data in config (nf-core#3190)
  New subworkflow: Fastq_fastp_trim_fastqc (nf-core#3146)

.github/workflows/nf-core-linting.yml

@@ -44,7 +44,7 @@ jobs:
         with:
           python-version: "3.x"
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
@@ -75,7 +75,7 @@ jobs:
         # HACK
         if: startsWith( matrix.tags, 'subworkflow' ) != true
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v3
         with:
           path: /usr/local/bin/nextflow
           key: ${{ runner.os }}

.github/workflows/nf-test.yml

@@ -0,0 +1,180 @@
+name: nf-test
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  merge_group:
+    types: [checks_requested]
+    branches: [master]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/nftest_modules.yml"
+
+  test:
+    runs-on: ubuntu-20.04
+
+    name: ${{ matrix.tags }} ${{ matrix.profile }}
+    needs: changes
+    if: needs.changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
+        profile: ["docker", "singularity", "conda"]
+        exclude:
+          - profile: "conda"
+            tags: bases2fastq
+          - profile: "conda"
+            tags: bcl2fastq
+          - profile: "conda"
+            tags: bclconvert
+          - profile: "conda"
+            tags: cellranger/count
+          - profile: "conda"
+            tags: cellranger/mkfastq
+          - profile: "conda"
+            tags: cellranger/mkgtf
+          - profile: "conda"
+            tags: cellranger/mkref
+          - profile: "conda"
+            tags: deepvariant
+          - profile: "conda"
+            tags: ensemblvep/vep
+          - profile: "conda"
+            tags: fastk/fastk
+          - profile: "conda"
+            tags: fastk/histex
+          - profile: "conda"
+            tags: fastk/merge
+          - profile: "conda"
+            tags: fcs/fcsadaptor
+          - profile: "conda"
+            tags: fcs/fcsgx
+          - profile: "conda"
+            tags: gatk4/cnnscorevariants
+          - profile: "conda"
+            tags: gatk4/determinegermlinecontigploidy
+          - profile: "conda"
+            tags: genescopefk
+          - profile: "conda"
+            tags: ilastik/multicut
+          - profile: "conda"
+            tags: ilastik/pixelclassification
+          - profile: "conda"
+            tags: imputeme/vcftoprs
+          - profile: "conda"
+            tags: merquryfk/katcomp
+          - profile: "conda"
+            tags: merquryfk/katgc
+          - profile: "conda"
+            tags: merquryfk/merquryfk
+          - profile: "conda"
+            tags: merquryfk/ploidyplot
+          - profile: "conda"
+            tags: sentieon/bwaindex
+          - profile: "conda"
+            tags: sentieon/bwamem
+          - profile: "conda"
+            tags: universc
+          - profile: "singularity"
+            tags: universc
+          - profile: "conda"
+            tags: subworkflows/vcf_annotate_ensemblvep
+    env:
+      NXF_ANSI_LOG: false
+      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+
+      # Set up secrets
+      - name: Set up nextflow secrets
+        if: env.SENTIEON_LICENSE_BASE64 != null
+        run: |
+          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
+          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
+          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
+          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
+          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
+
+      # Test the module
+      - name: Run nf-test
+        run: |
+          nf-test test \
+            --profile=${{ matrix.profile }} \
+            --tag ${{ matrix.tags }} \
+            --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap

.github/workflows/pytest-workflow.yml

@@ -98,6 +98,8 @@ jobs:
             tags: universc
           - profile: "conda"
             tags: subworkflows/vcf_annotate_ensemblvep
+          - profile: "conda"
+            tags: coreograph
     env:
       NXF_ANSI_LOG: false
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
@@ -109,7 +111,7 @@ jobs:
         with:
           python-version: "3.x"
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
@@ -119,7 +121,7 @@ jobs:
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow cryptography
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v3
         with:
           path: /usr/local/bin/nextflow
           key: ${{ runner.os }}

.gitignore

@@ -2,6 +2,7 @@
 work/
 results/
 test_output/
+.nf-test/
 output/
 .DS_Store
 *.code-workspace

modules/nf-core/art/illumina/main.nf

@@ -0,0 +1,71 @@
+process ART_ILLUMINA {
+
+    tag "$meta.id"
+    label 'process_single'
+
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    conda "bioconda::art=2016.06.05"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/art:2016.06.05--h589041f_9':
+        'quay.io/biocontainers/art:2016.06.05--h589041f_9' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    val(sequencing_system)
+    val(fold_coverage)
+    val(read_length)
+
+    output:
+    tuple val(meta), path("*.fq.gz"), emit: fastq
+    tuple val(meta), path("*.aln"), optional:true , emit: aln
+    tuple val(meta), path("*.sam"), optional:true , emit: sam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '2016.06.05' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    art_illumina \\
+        -ss $sequencing_system \\
+        -i $fasta \\
+        -l $read_length \\
+        -f $fold_coverage \\
+        -o $prefix \\
+        $args
+
+    gzip \\
+        --no-name \\
+        $args2 \\
+        $prefix*.fq
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        art: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '2016.06.05'
+    """
+    touch ${prefix}.fq.gz
+    touch ${prefix}1.fq.gz
+    touch ${prefix}2.fq.gz
+    touch ${prefix}.aln
+    touch ${prefix}1.aln
+    touch ${prefix}2.aln
+    touch ${prefix}.sam
+    touch ${prefix}1.sam
+    touch ${prefix}2.sam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        art: $VERSION
+    END_VERSIONS
+    """
+}

modules/nf-core/art/illumina/meta.yml

@@ -0,0 +1,61 @@
+name: "art_illumina"
+description: Simulation tool to generate synthetic Illumina next-generation sequencing reads
+keywords:
+  - fastq
+  - fasta
+  - illumina
+  - simulate
+tools:
+  - "art":
+      description: "ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. "
+      homepage: "https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm"
+      documentation: ""
+      tool_dev_url: ""
+      doi: "https://doi.org/10.1093/bioinformatics/btr708"
+      licence: "GPL version 3 license"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - fasta:
+      type: file
+      description: FASTA file of input DNA/RNA reference
+      pattern: "*.{fasta,fa}"
+  - sequencing_system:
+      type: string
+      description: The name of Illumina sequencing system of the built-in profile used for simulation
+  - fold_coverage:
+      type: integer
+      description: The fold of read coverage to be simulated or number of reads/read pairs generated for each amplicon
+  - read_length:
+      type: integer
+      description: The length of reads to be simulated
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fastq:
+      type: file
+      description: Simulated reads
+      pattern: "*.fq.gz"
+  - aln:
+      type: file
+      description: OPTIONAL Alignment file of the simulated reads. Enabled by default, to disable, use -na/--noALN.
+      pattern: "*.aln"
+  - sam:
+      type: file
+      description: OPTIONAL Alignment file in SAM format of the simulated reads. Enabled with -sam/--samout.
+      pattern: "*.sam"
+
+authors:
+  - "@MarieLataretu"

modules/nf-core/bwa/sampe/main.nf

@@ -31,7 +31,7 @@ process BWA_SAMPE {
         $read_group \\
         \$INDEX \\
         $sai \\
-        $reads | samtools sort -@ ${task.cpus - 1} -O bam - > ${prefix}.bam
+        $reads | samtools sort -@ ${task.cpus} -O bam - > ${prefix}.bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":