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modules.config
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modules.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Config file for defining DSL2 per module options and publishing paths
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Available keys to override module options:
ext.args = Additional arguments appended to command in module.
ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
ext.prefix = File name prefix for output files.
----------------------------------------------------------------------------------------
*/
def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []
//
// General configuration options
//
process {
publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
mode: params.publish_dir_mode,
pattern: '*_versions.yml'
]
}
}
//
// Genome preparation options
//
process {
withName: 'GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA' {
publishDir = [
path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
]
}
withName: 'UNTAR_.*' {
ext.args2 = '--no-same-owner'
}
withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
publishDir = [
path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
]
}
withName: 'GFFREAD' {
ext.args = '--keep-exon-attrs -F -T'
publishDir = [
path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
]
}
withName: 'HISAT2_EXTRACTSPLICESITES' {
publishDir = [
path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
]
}
withName: 'SALMON_INDEX' {
ext.args = { [
params.gencode ? '--gencode' : '',
params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}": ''
].join(' ').trim() }
publishDir = [
path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
]
}
withName: 'KALLISTO_INDEX' {
ext.args = params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}" : ''
publishDir = [
path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
]
}
withName: 'RSEM_PREPAREREFERENCE_GENOME' {
ext.args = '--star'
publishDir = [
path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
]
}
withName: 'GTF2BED' {
publishDir = [
path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
]
}
withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
publishDir = [
path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
]
}
withName: 'GTF_FILTER' {
ext.args = { params.skip_gtf_transcript_filter ?: '--skip_transcript_id_check' }
publishDir = [
path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
]
}
withName: 'CUSTOM_GETCHROMSIZES' {
publishDir = [
path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
]
}
withName: 'CAT_FASTQ' {
publishDir = [
path: { params.save_merged_fastq ? "${params.outdir}/fastq" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename.endsWith('.fastq.gz') && params.save_merged_fastq) ? filename : null }
]
}
}
if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
process {
withName: '.*:PREPARE_GENOME:BBMAP_BBSPLIT' {
ext.args = 'build=1'
publishDir = [
path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
mode: params.publish_dir_mode,
saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
]
}
}
}
//
// Read subsampling and strand inferring options
//
process {
withName: 'FQ_SUBSAMPLE' {
ext.args = '--record-count 1000000 --seed 1'
ext.prefix = { "${meta.id}.subsampled" }
publishDir = [
enabled: false
]
}
withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT' {
ext.args = '--skipQuant'
publishDir = [
enabled: false
]
}
}
//
// Read QC and trimming options
//
if (!(params.skip_fastqc || params.skip_qc)) {
if (params.trimmer == 'trimgalore') {
process {
withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
ext.args = '--quiet'
}
}
}
if (params.trimmer == 'fastp') {
process {
withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
ext.args = '--quiet'
}
withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
ext.args = '--quiet'
publishDir = [
path: { "${params.outdir}/${params.trimmer}/fastqc" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}
}
if (!params.skip_trimming) {
if (params.trimmer == 'trimgalore') {
process {
withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE' {
ext.args = {
[
"--fastqc_args '-t ${task.cpus}'",
params.extra_trimgalore_args ? params.extra_trimgalore_args.split("\\s(?=--)") : ''
].flatten().unique(false).join(' ').trim()
}
publishDir = [
[
path: { "${params.outdir}/${params.trimmer}/fastqc" },
mode: params.publish_dir_mode,
pattern: "*.{html,zip}"
],
[
path: { params.save_trimmed ? "${params.outdir}/${params.trimmer}" : params.outdir },
mode: params.publish_dir_mode,
pattern: "*.fq.gz",
saveAs: { params.save_trimmed ? it : null }
],
[
path: { "${params.outdir}/${params.trimmer}" },
mode: params.publish_dir_mode,
pattern: "*.txt"
]
]
}
}
}
if (params.trimmer == 'fastp') {
process {
withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
ext.args = { params.extra_fastp_args ?: '' }
publishDir = [
[
path: { "${params.outdir}/${params.trimmer}" },
mode: params.publish_dir_mode,
pattern: "*.{json,html}"
],
[
path: { "${params.outdir}/${params.trimmer}/log" },
mode: params.publish_dir_mode,
pattern: "*.log"
],
[
path: { params.save_trimmed ? "${params.outdir}/${params.trimmer}" : params.outdir },
mode: params.publish_dir_mode,
pattern: "*.fastq.gz",
saveAs: { params.save_trimmed ? it : null }
]
]
}
}
}
}
if (params.with_umi && !params.skip_umi_extract) {
process {
withName: 'UMITOOLS_EXTRACT' {
ext.args = { [
params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '',
params.umitools_bc_pattern ? "--bc-pattern='${params.umitools_bc_pattern}'" : '',
params.umitools_bc_pattern2 ? "--bc-pattern2='${params.umitools_bc_pattern2}'" : '',
params.umitools_umi_separator ? "--umi-separator='${params.umitools_umi_separator}'" : ''
].join(' ').trim() }
publishDir = [
[
path: { "${params.outdir}/umitools" },
mode: params.publish_dir_mode,
pattern: "*.log"
],
[
path: { params.save_umi_intermeds ? "${params.outdir}/umitools" : params.outdir },
mode: params.publish_dir_mode,
pattern: "*.fastq.gz",
saveAs: { params.save_umi_intermeds ? it : null }
]
]
}
}
}
//
// Contaminant removal options
//
if (!params.skip_bbsplit) {
process {
withName: 'BBMAP_BBSPLIT' {
ext.args = 'build=1 ambiguous2=all maxindel=150000'
publishDir = [
[
path: { "${params.outdir}/bbsplit" },
mode: params.publish_dir_mode,
pattern: '*.txt'
],
[
path: { params.save_bbsplit_reads ? "${params.outdir}/bbsplit" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
saveAs: { params.save_bbsplit_reads ? it : null }
]
]
}
}
}
if (params.remove_ribo_rna) {
process {
withName: 'SORTMERNA' {
ext.args = '--num_alignments 1 -v'
publishDir = [
[
path: { "${params.outdir}/sortmerna" },
mode: params.publish_dir_mode,
pattern: "*.log"
],
[
path: { params.save_non_ribo_reads ? "${params.outdir}/sortmerna" : params.outdir },
mode: params.publish_dir_mode,
pattern: "*.fastq.gz",
saveAs: { params.save_non_ribo_reads ? it : null }
]
]
}
}
}
//
// General alignment options
//
if (!params.skip_alignment) {
process {
withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
ext.prefix = { "${meta.id}.sorted.bam" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/samtools_stats" },
mode: params.publish_dir_mode,
pattern: "*.{stats,flagstat,idxstats}"
]
}
withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
ext.prefix = { "${meta.id}.sorted" }
publishDir = [
path: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
) || params.save_align_intermeds || params.skip_markduplicates ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: "*.bam",
saveAs: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
]
}
withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
ext.args = { params.bam_csi_index ? '-c' : '' }
publishDir = [
path: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
) || params.save_align_intermeds || params.skip_markduplicates ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: "*.{bai,csi}",
saveAs: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
]
}
}
if (!params.skip_markduplicates && !params.with_umi) {
process {
withName: '.*:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
ext.args = '--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
ext.prefix = { "${meta.id}.markdup.sorted" }
publishDir = [
[
path: { "${params.outdir}/${params.aligner}/picard_metrics" },
mode: params.publish_dir_mode,
pattern: '*metrics.txt'
],
[
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
pattern: '*.bam'
]
]
}
withName: '.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' {
ext.args = { params.bam_csi_index ? '-c' : '' }
ext.prefix = { "${meta.id}.markdup.sorted" }
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
pattern: '*.{bai,csi}'
]
}
withName: '.*:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
ext.prefix = { "${meta.id}.markdup.sorted.bam" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/samtools_stats" },
mode: params.publish_dir_mode,
pattern: '*.{stats,flagstat,idxstats}'
]
}
}
}
if (params.with_umi && ['star_salmon','hisat2'].contains(params.aligner)) {
process {
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
ext.args = { [
meta.single_end ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
params.umitools_umi_separator ? "--umi-separator='${params.umitools_umi_separator}'" : ''
].join(' ').trim() }
ext.prefix = { "${meta.id}.umi_dedup.sorted" }
publishDir = [
[
path: { "${params.outdir}/${params.aligner}/umitools" },
mode: params.publish_dir_mode,
pattern: '*.tsv'
],
[
path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.bam',
saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
]
]
}
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:SAMTOOLS_INDEX' {
ext.args = { params.bam_csi_index ? '-c' : '' }
ext.prefix = { "${meta.id}.umi_dedup.sorted" }
publishDir = [
path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.{bai,csi}',
saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
]
}
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
ext.prefix = { "${meta.id}.umi_dedup.sorted.bam" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/samtools_stats" },
mode: params.publish_dir_mode,
pattern: '*.{stats,flagstat,idxstats}'
]
}
}
}
if (!params.skip_bigwig) {
process {
withName: 'BEDTOOLS_GENOMECOV' {
ext.args = '-split -du'
publishDir = [
enabled: false
]
}
withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP' {
ext.prefix = { "${meta.id}.clip.forward" }
publishDir = [
enabled: false
]
}
withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
ext.prefix = { "${meta.id}.forward" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/bigwig" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP' {
ext.prefix = { "${meta.id}.clip.reverse" }
publishDir = [
enabled: false
]
}
withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
ext.prefix = { "${meta.id}.reverse" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/bigwig" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}
if (!params.skip_stringtie) {
process {
withName: 'STRINGTIE_STRINGTIE' {
ext.args = { [
'-v',
params.stringtie_ignore_gtf ? '' : '-e'
].join(' ').trim() }
publishDir = [
path: { "${params.outdir}/${params.aligner}/stringtie" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}
}
//
// STAR Salmon alignment options
//
if (!params.skip_alignment && params.aligner == 'star_salmon') {
process {
withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
ext.args = { [
'--quantMode TranscriptomeSAM',
'--twopassMode Basic',
'--outSAMtype BAM Unsorted',
'--readFilesCommand zcat',
'--runRNGseed 0',
'--outFilterMultimapNmax 20',
'--alignSJDBoverhangMin 1',
'--outSAMattributes NH HI AS NM MD',
'--quantTranscriptomeBan Singleend',
'--outSAMstrandField intronMotif',
params.save_unaligned ? '--outReadsUnmapped Fastx' : '',
params.extra_star_align_args ? params.extra_star_align_args.split("\\s(?=--)") : ''
].flatten().unique(false).join(' ').trim() }
publishDir = [
[
path: { "${params.outdir}/${params.aligner}/log" },
mode: params.publish_dir_mode,
pattern: '*.{out,tab}'
],
[
path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.bam',
saveAs: { params.save_align_intermeds ? it : null }
],
[
path: { params.save_unaligned ? "${params.outdir}/${params.aligner}/unmapped" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
saveAs: { params.save_unaligned ? it : null }
]
]
}
withName: '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT' {
ext.args = { params.extra_salmon_quant_args ?: '' }
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
]
}
withName: '.*:QUANTIFY_STAR_SALMON:TX2GENE' {
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: '.*:QUANTIFY_STAR_SALMON:TXIMPORT' {
ext.prefix = { "${quant_type}.merged" }
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: '.*:QUANTIFY_STAR_SALMON:SE_.*' {
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
if (params.with_umi) {
process {
withName: 'NFCORE_RNASEQ:RNASEQ:SAMTOOLS_SORT' {
ext.args = '-n'
ext.prefix = { "${meta.id}.umi_dedup.transcriptome" }
publishDir = [
path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.bam',
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
]
}
withName: 'NFCORE_RNASEQ:RNASEQ:UMITOOLS_PREPAREFORSALMON' {
ext.prefix = { "${meta.id}.umi_dedup.transcriptome.filtered" }
publishDir = [
[
path: { "${params.outdir}/${params.aligner}/umitools/log" },
mode: params.publish_dir_mode,
pattern: '*.log'
],
[
path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.bam',
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
]
]
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
ext.prefix = { "${meta.id}.transcriptome.sorted" }
publishDir = [
path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.bam',
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
]
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
publishDir = [
path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.bai',
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
]
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
ext.prefix = { "${meta.id}.transcriptome.sorted.bam" }
publishDir = [
path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}/samtools_stats" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.{stats,flagstat,idxstats}',
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
]
}
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
ext.args = { [
meta.single_end ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
params.umitools_umi_separator ? "--umi-separator='${params.umitools_umi_separator}'" : ''
].join(' ').trim() }
ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted" }
publishDir = [
[
path: { "${params.outdir}/${params.aligner}/umitools" },
mode: params.publish_dir_mode,
pattern: '*.tsv'
],
[
path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.bam',
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
]
]
}
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
publishDir = [
path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.bai',
saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
]
}
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*' {
ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted.bam" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/samtools_stats" },
mode: params.publish_dir_mode,
pattern: '*.{stats,flagstat,idxstats}'
]
}
}
}
if (!params.skip_qc & !params.skip_deseq2_qc) {
process {
withName: 'DESEQ2_QC_STAR_SALMON' {
ext.args = { [
"--id_col 1",
"--sample_suffix ''",
"--count_col 3",
params.deseq2_vst ? '--vst TRUE' : ''
].join(' ').trim() }
ext.args2 = 'star_salmon'
publishDir = [
path: { "${params.outdir}/${params.aligner}/deseq2_qc" },
mode: params.publish_dir_mode,
pattern: "*{RData,pca.vals.txt,plots.pdf,sample.dists.txt,size_factors,log}"
]
}
}
}
}
//
// STAR RSEM alignment options
//
if (!params.skip_alignment && params.aligner == 'star_rsem') {
process {
withName: '.*:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION' {
ext.args = [
'--star',
'--star-output-genome-bam',
'--star-gzipped-read-file',
'--estimate-rspd',
'--seed 1'
].join(' ').trim()
publishDir = [
[
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
pattern: "*.{stat,results}"
],
[
path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: "*.bam",
saveAs: { params.save_align_intermeds ? it : null }
],
[
path: { "${params.outdir}/${params.aligner}/log" },
mode: params.publish_dir_mode,
pattern: "*.log"
]
]
}
withName: '.*:QUANTIFY_RSEM:RSEM_MERGE_COUNTS' {
publishDir = [
path: { "${params.outdir}/${params.aligner}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
if (!params.skip_qc & !params.skip_deseq2_qc) {
process {
withName: 'DESEQ2_QC_RSEM' {
ext.args = { [
"--id_col 1",
"--sample_suffix ''",
"--count_col 3",
params.deseq2_vst ? '--vst TRUE' : ''
].join(' ').trim() }
ext.args2 = 'star_rsem'
publishDir = [
path: { "${params.outdir}/${params.aligner}/deseq2_qc" },
mode: params.publish_dir_mode,
pattern: "*{RData,pca.vals.txt,plots.pdf,sample.dists.txt,size_factors,log}"
]
}
}
}
}
//
// HISAT2 alignment options
//
if (!params.skip_alignment && params.aligner == 'hisat2') {
process {
withName: '.*:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN' {
ext.args = '--met-stderr --new-summary --dta'
publishDir = [
[
path: { "${params.outdir}/${params.aligner}/log" },
mode: params.publish_dir_mode,
pattern: '*.log'
],
[
path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.bam',
saveAs: { params.save_align_intermeds ? it : null }
],
[
path: { params.save_unaligned ? "${params.outdir}/${params.aligner}/unmapped" : params.outdir },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
saveAs: { params.save_unaligned ? it : null }
]
]
}
}
}
//
// Post-alignment QC options
//
if (!params.skip_alignment && !params.skip_qc) {
if (!params.skip_preseq) {
process {
withName: 'PRESEQ_LCEXTRAP' {
ext.args = '-verbose -bam -seed 1 -seg_len 100000000'
publishDir = [
[
path: { "${params.outdir}/${params.aligner}/preseq" },
mode: params.publish_dir_mode,
pattern: "*.txt"
],
[
path: { "${params.outdir}/${params.aligner}/preseq/log" },
mode: params.publish_dir_mode,
pattern: "*.log"
]
]
}
}
}
if (!params.skip_qualimap) {
process {
withName: 'QUALIMAP_RNASEQ' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/qualimap" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}
if (!params.skip_dupradar) {
process {
withName: 'DUPRADAR' {
publishDir = [
[
path: { "${params.outdir}/${params.aligner}/dupradar/scatter_plot" },
mode: params.publish_dir_mode,
pattern: "*Dens.pdf"
],
[
path: { "${params.outdir}/${params.aligner}/dupradar/box_plot" },
mode: params.publish_dir_mode,
pattern: "*Boxplot.pdf"
],
[
path: { "${params.outdir}/${params.aligner}/dupradar/histogram" },
mode: params.publish_dir_mode,
pattern: "*Hist.pdf"
],
[
path: { "${params.outdir}/${params.aligner}/dupradar/gene_data" },
mode: params.publish_dir_mode,
pattern: "*Matrix.txt"
],
[
path: { "${params.outdir}/${params.aligner}/dupradar/intercepts_slope" },
mode: params.publish_dir_mode,
pattern: "*slope.txt"
]
]
}
}
}
if (!params.skip_biotype_qc && params.featurecounts_group_type) {
process {
withName: 'SUBREAD_FEATURECOUNTS' {
ext.args = { [
'-B -C',
params.gencode ? "-g gene_type" : "-g $params.featurecounts_group_type",
"-t $params.featurecounts_feature_type"
].join(' ').trim() }
publishDir = [
path: { "${params.outdir}/${params.aligner}/featurecounts" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'MULTIQC_CUSTOM_BIOTYPE' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/featurecounts" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}
if (!params.skip_rseqc && 'bam_stat' in rseqc_modules) {
process {
withName: '.*:BAM_RSEQC:RSEQC_BAMSTAT' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/rseqc/bam_stat" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}
if (!params.skip_rseqc && 'infer_experiment' in rseqc_modules) {
process {
withName: '.*:BAM_RSEQC:RSEQC_INFEREXPERIMENT' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/rseqc/infer_experiment" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}
if (!params.skip_rseqc && 'junction_annotation' in rseqc_modules) {
process {
withName: '.*:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION' {
publishDir = [
[
path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/pdf" },
mode: params.publish_dir_mode,
pattern: '*.pdf'
],
[
path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/bed" },
mode: params.publish_dir_mode,
pattern: '*.bed'
],
[
path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/xls" },
mode: params.publish_dir_mode,
pattern: '*.xls'
],
[
path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/log" },
mode: params.publish_dir_mode,
pattern: '*.log'
],
[
path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/rscript" },
mode: params.publish_dir_mode,
pattern: '*.r'
]
]
}
}
}
if (!params.skip_rseqc && 'junction_saturation' in rseqc_modules) {
process {
withName: '.*:BAM_RSEQC:RSEQC_JUNCTIONSATURATION' {
publishDir = [
[
path: { "${params.outdir}/${params.aligner}/rseqc/junction_saturation/pdf" },
mode: params.publish_dir_mode,
pattern: '*.pdf'
],
[
path: { "${params.outdir}/${params.aligner}/rseqc/junction_saturation/rscript" },
mode: params.publish_dir_mode,
pattern: '*.r'
]
]
}
}
}
if (!params.skip_rseqc && 'read_duplication' in rseqc_modules) {