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Use module config
Signed-off-by: Ben Sherman <[email protected]>
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+1016
-1148
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15 files changed

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‎conf/modules.config‎

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‎main.nf‎

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@@ -59,7 +59,7 @@ WorkflowMain.initialise(workflow, params, log)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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include { RNASEQ } from './workflows/rnaseq'
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include { RNASEQ } from './workflows/rnaseq/main'
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//
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// WORKFLOW: Run main nf-core/rnaseq analysis pipeline

‎subworkflows/local/align_star/module.config‎

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withName: 'STAR_ALIGN|STAR_ALIGN_IGENOMES' {
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ext.args = { [
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'--quantMode TranscriptomeSAM',
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'--twopassMode Basic',
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'--outSAMtype BAM Unsorted',
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'--readFilesCommand zcat',
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'--runRNGseed 0',
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'--outFilterMultimapNmax 20',
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'--alignSJDBoverhangMin 1',
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'--outSAMattributes NH HI AS NM MD',
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'--quantTranscriptomeBan Singleend',
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'--outSAMstrandField intronMotif',
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params.save_unaligned ? '--outReadsUnmapped Fastx' : '',
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params.extra_star_align_args ? params.extra_star_align_args.split("\\s(?=--)") : ''
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].flatten().unique(false).join(' ').trim() }
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publishDir = [
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[
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path: { "${params.outdir}/${params.aligner}/log" },
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mode: params.publish_dir_mode,
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pattern: '*.{out,tab}'
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],
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[
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path: { "${params.outdir}/${params.aligner}" },
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mode: params.publish_dir_mode,
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pattern: '*.bam',
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saveAs: { params.save_align_intermeds ? it : null }
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],
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[
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path: { "${params.outdir}/${params.aligner}/unmapped" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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saveAs: { params.save_unaligned ? it : null }
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]
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]
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}

‎subworkflows/local/prepare_genome/module.config‎

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withName: 'GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA' {
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publishDir = [
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path: { "${params.outdir}/genome" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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withName: 'UNTAR_.*' {
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ext.args2 = '--no-same-owner'
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}
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withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
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publishDir = [
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path: { "${params.outdir}/genome/index" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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withName: 'GFFREAD' {
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ext.args = '--keep-exon-attrs -F -T'
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publishDir = [
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path: { "${params.outdir}/genome" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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withName: 'HISAT2_EXTRACTSPLICESITES' {
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publishDir = [
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path: { "${params.outdir}/genome/index" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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withName: 'SALMON_INDEX' {
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ext.args = params.gencode ? '--gencode' : ''
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publishDir = [
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path: { "${params.outdir}/genome/index" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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withName: 'RSEM_PREPAREREFERENCE_GENOME' {
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ext.args = '--star'
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publishDir = [
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path: { "${params.outdir}/genome/index" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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withName: 'GTF2BED' {
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publishDir = [
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path: { "${params.outdir}/genome" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
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publishDir = [
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path: { "${params.outdir}/genome" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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withName: 'GTF_GENE_FILTER' {
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publishDir = [
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path: { "${params.outdir}/genome" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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withName: 'CUSTOM_GETCHROMSIZES' {
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publishDir = [
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path: { "${params.outdir}/genome" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}
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withName: 'BBMAP_BBSPLIT' {
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ext.args = 'build=1'
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publishDir = [
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path: { "${params.outdir}/genome/index" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
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]
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}

‎subworkflows/local/quantify_rsem/module.config‎

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withName: 'RSEM_CALCULATEEXPRESSION' {
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ext.args = [
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'--star',
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'--star-output-genome-bam',
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'--star-gzipped-read-file',
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'--estimate-rspd',
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'--seed 1'
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].join(' ').trim()
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publishDir = [
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[
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path: { "${params.outdir}/${params.aligner}" },
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mode: params.publish_dir_mode,
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pattern: "*.{stat,results}"
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],
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[
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path: { "${params.outdir}/${params.aligner}" },
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mode: params.publish_dir_mode,
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pattern: "*.bam",
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saveAs: { params.save_align_intermeds ? it : null }
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],
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[
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path: { "${params.outdir}/${params.aligner}/log" },
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mode: params.publish_dir_mode,
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pattern: "*.log"
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]
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]
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}
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withName: 'RSEM_MERGE_COUNTS' {
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publishDir = [
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path: { "${params.outdir}/${params.aligner}" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}

‎subworkflows/local/quantify_salmon/module.config‎

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withName: 'SALMON_QUANT' {
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ext.args = { params.extra_salmon_quant_args ?: '' }
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publishDir = [
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path: { "${params.outdir}/${params.pseudo_aligner}" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
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]
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}
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withName: 'SALMON_TX2GENE' {
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publishDir = [
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path: { "${params.outdir}/${params.pseudo_aligner}" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: 'SALMON_TXIMPORT' {
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publishDir = [
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path: { "${params.outdir}/${params.pseudo_aligner}" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: 'SALMON_SE_.*' {
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publishDir = [
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path: { "${params.outdir}/${params.pseudo_aligner}" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}

‎subworkflows/nf-core/bam_markduplicates_picard/module.config‎

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‎subworkflows/nf-core/bam_rseqc/module.config‎

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