Run Nextflow lint in pre-commit

.github/workflows/lint.yml

@@ -36,6 +36,7 @@ jobs:
     runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: nf-core/setup-nextflow@v2
       - name: Run prek
         uses: j178/prek-action@0bb87d7f00b0c99306c8bcb8b8beba1eb581c037 # v1
 

.pre-commit-config.yaml

@@ -60,3 +60,11 @@ repos:
     hooks:
       - id: hadolint-docker
         args: ["--failure-threshold", "error"]
+
+  - repo: https://github.com/seqeralabs/nf-lint-pre-commit
+    rev: v0.2.0
+    hooks:
+      - id: nextflow-lint
+        files: '\.nf$|nextflow\.config$'
+        # TODO add formating at a later stage
+        # args: ["-format", "-sort-declarations", "-spaces", "4", "-harshil-alignment", "-output", "concise"]

modules/nf-core/abricate/summary/main.nf

@@ -22,7 +22,7 @@ process ABRICATE_SUMMARY {
     """
     abricate \\
         --summary \\
-        ${reports} > ${prefix}.txt
+        $reports > ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/agrvate/main.nf

@@ -22,8 +22,8 @@ process AGRVATE {
     def args = task.ext.args   ?: ''
     """
     agrvate \\
-        ${args} \\
-        -i ${fasta}
+        $args \\
+        -i $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/allelecounter/main.nf

@@ -25,10 +25,10 @@ process ALLELECOUNTER {
     def reference_options = fasta ? "-r $fasta": ""
     """
     alleleCounter \\
-        ${args} \\
-        -l ${loci} \\
-        -b ${input} \\
-        ${reference_options} \\
+        $args \\
+        -l $loci \\
+        -b $input \\
+        $reference_options \\
         -o ${prefix}.alleleCount
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/ampcombi2/cluster/main.nf

@@ -24,7 +24,7 @@ process AMPCOMBI2_CLUSTER {
     """
     ampcombi cluster \\
         --ampcombi_summary ${summary_file} \\
-        ${args} \\
+        $args \\
         --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/amplify/predict/main.nf

@@ -25,7 +25,7 @@ process AMPLIFY_PREDICT {
     def custom_model_dir = model_dir ? "-md ${model_dir}" : ""
     """
     AMPlify \\
-        ${args} \\
+        $args \\
         ${custom_model_dir} \\
         -s '${faa}'
 

modules/nf-core/angsd/contamination/tests/nextflow.config

@@ -2,4 +2,4 @@ process {
     withName: ANGSD_DOCOUNTS {
         ext.args = "-iCounts 1 -doDepth -dumpCounts 2"
     }
-}
+}

modules/nf-core/aria2/main.nf

@@ -24,8 +24,8 @@ process ARIA2 {
     """
     aria2c \\
         --check-certificate=false \\
-        ${args} \\
-        ${source_url}
+        $args \\
+        $source_url
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/artic/guppyplex/main.nf

@@ -23,11 +23,11 @@ process ARTIC_GUPPYPLEX {
     """
     artic \\
         guppyplex \\
-        ${args} \\
-        --directory ${fastq_dir} \\
+        $args \\
+        --directory $fastq_dir \\
         --output ${prefix}.fastq
 
-    pigz -p ${task.cpus} *.fastq
+    pigz -p $task.cpus *.fastq
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         artic: \$(artic -v 2>&1 | sed 's/^.*artic //; s/ .*\$//')

modules/nf-core/ataqv/mkarv/main.nf

@@ -20,8 +20,8 @@ process ATAQV_MKARV {
     def args = task.ext.args ?: ''
     """
     mkarv \\
-        ${args} \\
-        --concurrency ${task.cpus} \\
+        $args \\
+        --concurrency $task.cpus \\
         --force \\
         ./html/ \\
         jsons/*

modules/nf-core/atlas/recal/main.nf

@@ -31,13 +31,13 @@ process ATLAS_RECAL {
     """
     atlas \\
         task=recal \\
-        bam=${bam} \\
-        ${PMD} \\
-        ${READGROUPS} \\
-        ${ALLELES} \\
-        ${INVARIANTS} \\
-        out=${prefix} \\
-        ${args}
+        bam=$bam \\
+        $PMD \\
+        $READGROUPS \\
+        $ALLELES \\
+        $INVARIANTS \\
+        out=$prefix \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/authentict/deam2cont/main.nf

@@ -27,11 +27,11 @@ process AUTHENTICT_DEAM2CONT {
     def positions_file = positions ? "-p ${positions}" : ""
 
     """
-    samtools view ${args} ${bam} | AuthentiCT \\
+    samtools view $args $bam | AuthentiCT \\
         deam2cont \\
-        ${args2} \\
-        ${config_file} \\
-        ${positions_file} \\
+        $args2 \\
+        $config_file \\
+        $positions_file \\
         - \\
         > ${prefix}.txt
 

modules/nf-core/bcftools/call/tests/nextflow.config

@@ -1,3 +1,3 @@
 process {
     ext.args = "--no-version"
-}
+}

modules/nf-core/bcftools/mpileup/tests/nextflow.config

@@ -1,4 +1,4 @@
 process {
     ext.args2 = '--no-version --ploidy 1 --multiallelic-caller'
     ext.args3 = '--no-version'
-}
+}

modules/nf-core/bcftools/query/tests/nextflow.config

@@ -1,3 +1,3 @@
 process {
     ext.args = "-f '%CHROM %POS %REF %ALT[%SAMPLE=%GT]'"
-}
+}

modules/nf-core/blat/tests/nextflow.config

@@ -2,4 +2,4 @@ process {
     withName: SEQTK_SEQ {
         ext.args = '-A'
     }
-}
+}

modules/nf-core/bowtie/build/main.nf

@@ -11,8 +11,8 @@ process BOWTIE_BUILD {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path('bowtie'), emit: index
-    path "versions.yml", emit: versions
+    tuple val(meta), path('bowtie') , emit: index
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,7 +21,7 @@ process BOWTIE_BUILD {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p bowtie
-    bowtie-build --threads ${task.cpus} ${fasta} bowtie/${prefix}
+    bowtie-build --threads $task.cpus $fasta bowtie/${prefix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -45,4 +45,5 @@ process BOWTIE_BUILD {
         bowtie: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
     END_VERSIONS
     """
+
 }

modules/nf-core/calder2/tests/nextflow.config

@@ -1,3 +1,3 @@
 process {
     ext.args = '--genome hg38'
-}
+}

modules/nf-core/cellranger/mkref/tests/nextflow.config

@@ -3,3 +3,4 @@ process {
         publishDir = [ path: { "output" } ]
     }
 }
+

modules/nf-core/checkm2/predict/tests/nextflow.config

@@ -2,4 +2,4 @@ process {
     withName: "CHECKM2_PREDICT" {
         ext.args = "--lowmem"
     }
-}
+}

modules/nf-core/clame/tests/nextflow.config

@@ -2,4 +2,4 @@ process {
     withName: CLAME {
         ext.args = '-b 100 -print'
     }
-}
+}

modules/nf-core/cnvkit/export/tests/nextflow.config

@@ -2,4 +2,4 @@ process {
     withName: 'CNVKIT_EXPORT' {
         ext.args = { params.cnvkit_export_args }
     }
-}
+}

modules/nf-core/controlfreec/assesssignificance/main.nf

@@ -1,47 +1,45 @@
 process CONTROLFREEC_ASSESSSIGNIFICANCE {
-    tag "${meta.id}"
+    tag "$meta.id"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0'
-        : 'biocontainers/control-freec:11.6b--hdbdd923_0'}"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' :
+        'biocontainers/control-freec:11.6b--hdbdd923_0' }"
 
     input:
     tuple val(meta), path(cnvs), path(ratio)
 
     output:
     tuple val(meta), path("*.p.value.txt"), emit: p_value_txt
-    path "versions.yml", emit: versions
+    path "versions.yml"                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '11.6b'
-    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     cat \$(which assess_significance.R) | R --slave --args ${cnvs} ${ratio}
 
     mv *.p.value.txt ${prefix}.p.value.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: ${VERSION}
+        controlfreec: $VERSION
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '11.6b'
-    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.p.value.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: ${VERSION}
+        controlfreec: $VERSION
     END_VERSIONS
     """
 }

modules/nf-core/controlfreec/freec2bed/main.nf

@@ -1,46 +1,44 @@
 process CONTROLFREEC_FREEC2BED {
-    tag "${meta.id}"
+    tag "$meta.id"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0'
-        : 'biocontainers/control-freec:11.6b--hdbdd923_0'}"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' :
+        'biocontainers/control-freec:11.6b--hdbdd923_0' }"
 
     input:
     tuple val(meta), path(ratio)
 
     output:
     tuple val(meta), path("*.bed"), emit: bed
-    path "versions.yml", emit: versions
+    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 VERSION = '11.6b'
-    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     freec2bed.pl -f ${ratio} ${args} > ${prefix}.bed
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: ${VERSION}
+        controlfreec: $VERSION
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '11.6b'
-    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.bed
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        controlfreec: ${VERSION}
+        controlfreec: $VERSION
     END_VERSIONS
     """
 }