mirror of
https://github.com/MillironX/nf-core_modules.git
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commit
deb0a103db
3 changed files with 31 additions and 11 deletions
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@ -5,7 +5,7 @@ params.options = [:]
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def options = initOptions(params.options)
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def options = initOptions(params.options)
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process SALMON_INDEX {
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process SALMON_INDEX {
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tag "$fasta"
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tag "$transcript_fasta"
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label "process_medium"
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label "process_medium"
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publishDir "${params.outdir}",
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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@ -15,7 +15,8 @@ process SALMON_INDEX {
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container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
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container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
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input:
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input:
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path fasta
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path genome_fasta
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path transcript_fasta
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output:
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output:
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path "salmon" , emit: index
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path "salmon" , emit: index
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@ -23,11 +24,22 @@ process SALMON_INDEX {
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script:
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script:
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def software = getSoftwareName(task.process)
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def software = getSoftwareName(task.process)
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def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt"
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def gentrome = "gentrome.fa"
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if (genome_fasta.endsWith('.gz')) {
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get_decoy_ids = "grep '^>' <(gunzip -c $genome_fasta) | cut -d ' ' -f 1 > decoys.txt"
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gentrome = "gentrome.fa.gz"
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}
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"""
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"""
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$get_decoy_ids
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sed -i.bak -e 's/>//g' decoys.txt
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cat $transcript_fasta $genome_fasta > $gentrome
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salmon \\
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salmon \\
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index \\
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index \\
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--threads $task.cpus \\
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--threads $task.cpus \\
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-t $fasta \\
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-t gentrome.fa \\
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-d decoys.txt \\
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$options.args \\
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$options.args \\
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-i salmon
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-i salmon
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salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
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salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
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@ -18,6 +18,8 @@ process SALMON_QUANT {
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tuple val(meta), path(reads)
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tuple val(meta), path(reads)
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path index
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path index
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path gtf
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path gtf
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path transcript_fasta
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val alignment_mode
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output:
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output:
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tuple val(meta), path("${prefix}"), emit: results
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tuple val(meta), path("${prefix}"), emit: results
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@ -26,7 +28,13 @@ process SALMON_QUANT {
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script:
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script:
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def software = getSoftwareName(task.process)
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def software = getSoftwareName(task.process)
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def endedness = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
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def reference = "--index $index"
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def input_reads = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
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if (alignment_mode) {
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reference = "-t $transcript_fasta"
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input_reads = "-a $reads"
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}
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def strandedness = meta.single_end ? 'U' : 'IU'
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def strandedness = meta.single_end ? 'U' : 'IU'
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if (meta.strandedness == 'forward') {
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if (meta.strandedness == 'forward') {
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@ -39,8 +47,8 @@ process SALMON_QUANT {
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--geneMap $gtf \\
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--geneMap $gtf \\
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--threads $task.cpus \\
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--threads $task.cpus \\
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--libType=$strandedness \\
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--libType=$strandedness \\
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--index $index \\
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$reference \\
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$endedness \\
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$input_reads \\
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$options.args \\
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$options.args \\
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-o $prefix
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-o $prefix
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@ -6,7 +6,7 @@ def options = initOptions(params.options)
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def VERSION = '377'
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def VERSION = '377'
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process UCSC_BEDRAPHTOBIGWIG {
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process UCSC_BEDGRAPHTOBIGWIG {
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tag "$meta.id"
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tag "$meta.id"
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label 'process_medium'
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label 'process_medium'
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publishDir "${params.outdir}",
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publishDir "${params.outdir}",
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