Merge pull request #20 from nf-core/nfcore-style-adjustments

Adjustments to better match nf-core standards
nf-core · May 3, 2024 · d8bbe1c · d8bbe1c
2 parents fa95510 + e11a387
commit d8bbe1c
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Showing 73 changed files with 3,289 additions and 3,208 deletions.
diff --git a/modules/local/amber/main.nf b/modules/local/amber/main.nf
@@ -5,7 +5,7 @@ process AMBER {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-amber:4.0--hdfd78af_0' :
-        'quay.io/biocontainers/hmftools-amber:4.0--hdfd78af_0' }"
+        'biocontainers/hmftools-amber:4.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(tumor_bam), path(normal_bam), path(tumor_bai), path(normal_bai)
@@ -52,6 +52,7 @@ process AMBER {
     """
     mkdir -p amber/
     touch amber/placeholder
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/bamtools/main.nf b/modules/local/bamtools/main.nf
@@ -5,7 +5,7 @@ process BAMTOOLS {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-bam-tools:1.2.1--hdfd78af_0' :
-        'quay.io/biocontainers/hmftools-bam-tools:1.2.1--hdfd78af_0' }"
+        'biocontainers/hmftools-bam-tools:1.2.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -26,6 +26,7 @@ process BAMTOOLS {
     bamtools \\
         -Xmx${Math.round(task.memory.bytes * 0.95)} \\
         com.hartwig.hmftools.bamtools.metrics.BamMetrics \\
+        ${args} \\
         -sample ${meta.sample_id} \\
         -bam_file ${bam} \\
         -ref_genome ${genome_fasta} \\
@@ -44,6 +45,7 @@ process BAMTOOLS {
     stub:
     """
     touch ${meta.sample_id}.wgsmetrics
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/bwa-mem2/mem/main.nf b/modules/local/bwa-mem2/mem/main.nf
@@ -5,7 +5,7 @@ process BWAMEM2_ALIGN {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' :
-        'quay.io/biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' }"
+        'biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' }"
 
     input:
     tuple val(meta), path(reads_fwd), path(reads_rev)

diff --git a/modules/local/chord/main.nf b/modules/local/chord/main.nf
@@ -5,7 +5,7 @@ process CHORD {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/r-chord:2.03--r43hdfd78af_0' :
-        'quay.io/biocontainers/r-chord:2.03--r43hdfd78af_0' }"
+        'biocontainers/r-chord:2.03--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(smlv_vcf), path(sv_vcf)
@@ -19,8 +19,6 @@ process CHORD {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-
     """
     #!/usr/bin/env Rscript
     library('CHORD')
@@ -82,6 +80,7 @@ process CHORD {
     mkdir -p chord/
     touch chord/${meta.sample_id}_chord_signatures.txt
     touch chord/${meta.sample_id}_chord_prediction.txt
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/cobalt/main.nf b/modules/local/cobalt/main.nf
@@ -5,7 +5,7 @@ process COBALT {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-cobalt:1.16--hdfd78af_0' :
-        'quay.io/biocontainers/hmftools-cobalt:1.16--hdfd78af_0' }"
+        'biocontainers/hmftools-cobalt:1.16--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(tumor_bam), path(normal_bam), path(tumor_bai), path(normal_bai)

diff --git a/modules/local/cuppa/main.nf b/modules/local/cuppa/main.nf
@@ -5,7 +5,7 @@ process CUPPA {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-cuppa:1.8.1--hdfd78af_0' :
-        'quay.io/biocontainers/hmftools-cuppa:1.8.1--hdfd78af_0' }"
+        'biocontainers/hmftools-cuppa:1.8.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(isofox_dir), path(purple_dir), path(linx_dir), path(virusinterpreter_dir)
@@ -46,6 +46,7 @@ process CUPPA {
 
     cuppa \\
         -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        ${args} \\
         -sample ${meta.sample_id} \\
         -sample_data_dir sample_data/ \\
         -categories ${classifier} \\
@@ -76,6 +77,7 @@ process CUPPA {
     touch cuppa/${meta.sample_id}.cup.report.summary.png
     touch cuppa/${meta.sample_id}.cup.report.features.png
     touch cuppa/${meta.sample_id}.cuppa.chart.png
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/custom/lilac_extract_and_index_contig/main.nf b/modules/local/custom/lilac_extract_and_index_contig/main.nf
@@ -5,7 +5,7 @@ process CUSTOM_EXTRACTCONTIG {
     conda "bwa-mem2=2.2.1 samtools=1.19.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' :
-        'quay.io/biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' }"
+        'biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' }"
 
     input:
     val contig_name

diff --git a/modules/local/custom/lilac_realign_reads_lilac/main.nf b/modules/local/custom/lilac_realign_reads_lilac/main.nf
@@ -5,7 +5,7 @@ process CUSTOM_REALIGNREADS {
     conda "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.19.2 bioconda::sambamba=1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' :
-        'quay.io/biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' }"
+        'biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

diff --git a/modules/local/custom/lilac_slice/main.nf b/modules/local/custom/lilac_slice/main.nf
@@ -5,7 +5,7 @@ process CUSTOM_SLICE {
     conda "samtools=1.19.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
-        'quay.io/biocontainers/samtools:1.19.2--h50ea8bc_0' }"
+        'biocontainers/samtools:1.19.2--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

diff --git a/modules/local/fastp/environment.yml b/modules/local/fastp/environment.yml
@@ -0,0 +1,7 @@
+name: fastp
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::fastp=0.23.4
diff --git a/modules/local/fastp/main.nf b/modules/local/fastp/main.nf
@@ -1,13 +1,15 @@
 process FASTP {
     tag "${meta.id}"
+    label 'process_medium'
 
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastp:0.23.4--hadf994f_2' :
-        'quay.io/biocontainers/fastp:0.23.4--hadf994f_2' }"
+        'biocontainers/fastp:0.23.4--hadf994f_2' }"
 
     input:
     tuple val(meta), path(reads_fwd), path(reads_rev)
-    val(max_fastq_records)
+    val max_fastq_records
 
     output:
     tuple val(meta), path('*_R1.fastp.fastq.gz'), path('*_R2.fastp.fastq.gz'), emit: fastq
@@ -17,12 +19,11 @@ process FASTP {
     task.ext.when == null || task.ext.when
 
     script:
-    """
-    # * do not apply trimming/clipping, already done in BCL convert
-    # * turn off all filtering
-    # * do not process umis, already done for us
+    def args = task.ext.args ?: ''
 
+    """
     fastp \\
+        ${args} \\
         --in1 ${reads_fwd} \\
         --in2 ${reads_rev} \\
         --disable_quality_filtering \\

diff --git a/modules/local/gridss/index/main.nf b/modules/local/gridss/index/main.nf
@@ -6,7 +6,7 @@ process GRIDSS_INDEX {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gridss:2.13.2--h50ea8bc_3' :
-        'quay.io/biocontainers/gridss:2.13.2--h50ea8bc_3' }"
+        'biocontainers/gridss:2.13.2--h50ea8bc_3' }"
 
     input:
     path genome_fasta

diff --git a/modules/local/gripss/germline/main.nf b/modules/local/gripss/germline/main.nf
@@ -5,7 +5,7 @@ process GRIPSS_GERMLINE {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-gripss:2.4--hdfd78af_0' :
-        'quay.io/biocontainers/hmftools-gripss:2.4--hdfd78af_0' }"
+        'biocontainers/hmftools-gripss:2.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gridss_vcf)
@@ -57,6 +57,7 @@ process GRIPSS_GERMLINE {
     touch ${meta.normal_id}.gripss.filtered.germline.vcf.gz.tbi
     touch ${meta.normal_id}.gripss.germline.vcf.gz
     touch ${meta.normal_id}.gripss.germline.vcf.gz.tbi
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/gripss/somatic/main.nf b/modules/local/gripss/somatic/main.nf
@@ -5,7 +5,7 @@ process GRIPSS_SOMATIC {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-gripss:2.4--hdfd78af_0' :
-        'quay.io/biocontainers/hmftools-gripss:2.4--hdfd78af_0' }"
+        'biocontainers/hmftools-gripss:2.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gridss_vcf)
@@ -62,6 +62,7 @@ process GRIPSS_SOMATIC {
     touch ${meta.tumor_id}.gripss.filtered.somatic.vcf.gz.tbi
     touch ${meta.tumor_id}.gripss.somatic.vcf.gz
     touch ${meta.tumor_id}.gripss.somatic.vcf.gz.tbi
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/isofox/main.nf b/modules/local/isofox/main.nf
@@ -5,7 +5,7 @@ process ISOFOX {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-isofox:1.7.1--hdfd78af_0':
-        'quay.io/biocontainers/hmftools-isofox:1.7.1--hdfd78af_0' }"
+        'biocontainers/hmftools-isofox:1.7.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -68,6 +68,7 @@ process ISOFOX {
     """
     mkdir -p isofox/
     touch isofox/placeholder
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/lilac/main.nf b/modules/local/lilac/main.nf
@@ -5,7 +5,7 @@ process LILAC {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-lilac:1.6--hdfd78af_0' :
-        'quay.io/biocontainers/hmftools-lilac:1.6--hdfd78af_0' }"
+        'biocontainers/hmftools-lilac:1.6--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(normal_dna_bam), path(normal_dna_bai), path(tumor_dna_bam), path(tumor_dna_bai), path(tumor_rna_bam), path(tumor_rna_bai), path(purple_dir)
@@ -55,6 +55,7 @@ process LILAC {
     """
     mkdir -p lilac/
     touch lilac/placeholder
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }

diff --git a/modules/local/linx/germline/main.nf b/modules/local/linx/germline/main.nf
@@ -5,7 +5,7 @@ process LINX_GERMLINE {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-linx:1.25--hdfd78af_0':
-        'quay.io/biocontainers/hmftools-linx:1.25--hdfd78af_0' }"
+        'biocontainers/hmftools-linx:1.25--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(sv_vcf)
@@ -45,6 +45,7 @@ process LINX_GERMLINE {
     """
     mkdir linx_germline/
     touch linx_germline/placeholder
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/linx/somatic/main.nf b/modules/local/linx/somatic/main.nf
@@ -5,7 +5,7 @@ process LINX_SOMATIC {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-linx:1.25--hdfd78af_0':
-        'quay.io/biocontainers/hmftools-linx:1.25--hdfd78af_0' }"
+        'biocontainers/hmftools-linx:1.25--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(purple_dir)
@@ -48,6 +48,7 @@ process LINX_SOMATIC {
     """
     mkdir linx_somatic/
     touch linx_somatic/placeholder
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/linx/visualiser/main.nf b/modules/local/linx/visualiser/main.nf
@@ -5,7 +5,7 @@ process LINX_VISUALISER {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-linx:1.25--hdfd78af_0':
-        'quay.io/biocontainers/hmftools-linx:1.25--hdfd78af_0' }"
+        'biocontainers/hmftools-linx:1.25--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(linx_annotation_dir)
@@ -93,6 +93,7 @@ process LINX_VISUALISER {
     """
     mkdir -p plots/{all,reportable}/
     touch plots/{all,reportable}/placeholder
+
     echo -e '${task.process}:\n  stub: noversions\n' > versions.yml
     """
 }
diff --git a/modules/local/linxreport/main.nf b/modules/local/linxreport/main.nf
@@ -5,7 +5,7 @@ process LINXREPORT {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/r-linxreport:1.0.0--r43hdfd78af_0' :
-        'quay.io/biocontainers/r-linxreport:1.0.0--r43hdfd78af_0' }"
+        'biocontainers/r-linxreport:1.0.0--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(linx_annotation_dir), path(linx_visualiser_dir)
@@ -45,6 +45,7 @@ process LINXREPORT {
     stub:
     """
     touch ${meta.sample_id}_linx.html
+
     echo -e '${task.process}:\n  stub: noversions\n' > versions.yml
     """
 }
diff --git a/modules/local/markdups/environment.yml b/modules/local/markdups/environment.yml
@@ -0,0 +1,7 @@
+name: markdups
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::hmftools-mark-dups=1.1.5
diff --git a/modules/local/markdups/main.nf b/modules/local/markdups/main.nf
@@ -4,7 +4,7 @@ process MARKDUPS {
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-mark-dups:1.1.5--hdfd78af_0' :
-        'quay.io/biocontainers/hmftools-mark-dups:1.1.5--hdfd78af_0' }"
+        'biocontainers/hmftools-mark-dups:1.1.5--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams), path(bais)
@@ -24,10 +24,12 @@ process MARKDUPS {
     task.ext.when == null || task.ext.when
 
     script:
+    def args = task.ext.args ?: ''
     def umi_flags = has_umis ? '-umi_enabled -umi_duplex -umi_duplex_delim +' : ''
 
     """
     markdups \\
+        ${args} \\
         -Xmx${Math.round(task.memory.bytes * 0.95)} \\
         \\
         -samtools \$(which samtools) \\

diff --git a/modules/local/orange/main.nf b/modules/local/orange/main.nf
@@ -5,7 +5,7 @@ process ORANGE {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-orange:2.7.1--hdfd78af_0' :
-        'quay.io/biocontainers/hmftools-orange:2.7.1--hdfd78af_0' }"
+        'biocontainers/hmftools-orange:2.7.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam_metrics_somatic), path(bam_metrics_germline), path(flagstat_somatic), path(flagstat_germline), path(sage_somatic_dir), path(sage_germline_dir), path(smlv_somatic_vcf), path(smlv_germline_vcf), path(purple_dir), path(linx_somatic_anno_dir), path(linx_somatic_plot_dir), path(linx_germline_anno_dir), path(virusinterpreter_dir), path(chord_dir), path(sigs_dir), path(lilac_dir), path(cuppa_dir), path(isofox_dir)
@@ -105,6 +105,7 @@ process ORANGE {
         --add-opens java.base/java.time=ALL-UNNAMED \\
         -Xmx${Math.round(task.memory.bytes * 0.95)} \\
         -jar \${orange_jar} \\
+            ${args} \\
             \\
             -experiment_date \$(date +%y%m%d) \\
             -add_disclaimer \\
@@ -156,6 +157,7 @@ process ORANGE {
     mkdir -p output/
     touch output/${meta.tumor_id}.orange.json
     touch output/${meta.tumor_id}.orange.pdf
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/pave/germline/main.nf b/modules/local/pave/germline/main.nf
@@ -9,7 +9,7 @@ process PAVE_GERMLINE {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmftools-pave:1.6--hdfd78af_0' :
-        'quay.io/biocontainers/hmftools-pave:1.6--hdfd78af_0' }"
+        'biocontainers/hmftools-pave:1.6--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(sage_vcf), path(sage_tbi)
@@ -73,6 +73,7 @@ process PAVE_GERMLINE {
     stub:
     """
     touch ${meta.sample_id}.sage.pave_germline.vcf.gz{,.tbi}
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }