Update syntax for most modules

.github/workflows/lint-code.yml

@@ -46,7 +46,7 @@ jobs:
       - name: Install NodeJS
         uses: actions/setup-node@v1
         with:
-          node-version: "10"
+          node-version: "12.9.0"
 
       - name: Install yaml-lint
         run: npm install -g yaml-lint

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

@@ -57,7 +57,7 @@ jobs:
 
         # FIXME: Remove this when nf-core modules lint stabilizes and install stable release
       - name: Install nf-core tools development version
-        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@2.1
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@2.3.2
 
       - name: Install Nextflow
         env:

.github/workflows/test-modules.yml

@@ -91,13 +91,13 @@ jobs:
       # Test the module
       - name: Run pytest-workflow
         # only use one thread for pytest-workflow to avoid race condition on conda cache.
-        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware
 
       - name: Upload logs on failure
         if: failure()
         uses: actions/upload-artifact@v2
         with:
-          name: logs-${{ matrix.tags }}-${{ matrix.profile }}-${{ matrix.nxf_version }}
+          name: logs-${{ matrix.profile }}-${{ matrix.nxf_version }}
           path: |
             /home/runner/pytest_workflow_*/*/.nextflow.log
             /home/runner/pytest_workflow_*/*/log.out

.nf-core.yml

@@ -0,0 +1 @@
+repository_type: modules

modules/clippy/main.nf

@@ -1,46 +1,43 @@
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
 process CLIPPY {
     tag "$meta.id"
     label "avg_cores"
-    label "high_mem"
+    label "avg_mem"
     label "regular_queue"
-    publishDir "${params.outdir}",
-        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::clippy=1.3.1" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/clippy:1.3.1--pyhdfd78af_2"
-    } else {
-        container "quay.io/biocontainers/clippy:1.3.1--pyhdfd78af_2"
-    }
+    conda (params.enable_conda ? "bioconda::clippy=1.4.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/clippy:1.4.1--pyhdfd78af_1' :
+        'quay.io/biocontainers/clippy:1.4.1--pyhdfd78af_1' }"
 
     input:
     tuple val(meta), path(crosslinks)
     path(gtf)
     path(fai)
 
     output:
-    tuple val(meta), path("*_broadPeaks.bed.gz"), emit: peaks
-    tuple val(meta), path("*[0-9].bed.gz"),       emit: summits
-    path "*.version.txt",                         emit: version
+    tuple val(meta), path("*_Peaks.bed.gz"),           emit: peaks
+    tuple val(meta), path("*_Summits.bed.gz"),         emit: summits
+    tuple val(meta), path("*_intergenic_regions.gtf"), emit: intergenic_gtf, optional: true
+    path "versions.yml",                               emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
 
     script:
-    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args = task.ext.args ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
     """
     clippy -i $crosslinks \
         -o $prefix \
         -a $gtf \
         -g $fai \
         -t ${task.cpus} \
-        $options.args
-    gzip -n *_broadPeaks.bed
-    gzip -n *[0-9].bed
-    echo \$(clippy -v) > ${software}.version.txt
+        $args
+    gzip -n *_Peaks.bed
+    gzip -n *_Summits.bed
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        clippy: \$(clippy -v)
+    END_VERSIONS
     """
 }

modules/crosslinks/coverage/main.nf

@@ -1,40 +1,35 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-params.options = [:]
-options        = initOptions(params.options)
-
 process CROSSLINKS_COVERAGE {
     tag "$meta.id"
     label "low_cores"
     label "low_mem"
     label "regular_queue"
-    publishDir "${params.outdir}",
-        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 ? "conda-forge::sed=4.7" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
-    } else {
-        container "biocontainers/biocontainers:v1.2.0_cv1"
-    }
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+        'biocontainers/biocontainers:v1.2.0_cv1' }"
 
     input:
     tuple val(meta), path(crosslinks)
 
     output:
-    tuple val(meta), path("*.bedgraph.gz"), emit: bedgraph
-    path "*.version.txt",                   emit: version
+    tuple val(meta), path("$prefix*.bedgraph.gz"), emit: bedgraph
+    path "versions.yml",                           emit: versions
 
-    script:
-    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    when:
+    task.ext.when == null || task.ext.when
 
+    script:
+    def args = task.ext.args ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
     """
     gzip -d -c $crosslinks | \
         awk '{OFS = "\t"}{if (\$6 == "+") {print \$1, \$2, \$3, \$5} else {print \$1, \$2, \$3, -\$5}}' | \
         gzip > ${prefix}.bedgraph.gz
 
-    echo \$(awk --version 2>&1) | sed 's/^.*awk version //' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+    END_VERSIONS
     """
 }