nf-core_modules/modules/star/align/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process STAR_ALIGN {
tag "$meta.id"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? 'bioconda::star=2.7.9a' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/star:2.7.9a--h9ee0642_0'
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} else {
container 'quay.io/biocontainers/star:2.7.9a--h9ee0642_0'
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}
input:
tuple val(meta), path(reads)
path index
path gtf
output:
tuple val(meta), path('*d.out.bam') , emit: bam
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tuple val(meta), path('*Log.final.out') , emit: log_final
tuple val(meta), path('*Log.out') , emit: log_out
tuple val(meta), path('*Log.progress.out'), emit: log_progress
path '*.version.txt' , emit: version
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tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted
tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript
tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted
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tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq
tuple val(meta), path('*.tab') , optional:true, emit: tab
tuple val(meta), path('*.out.junction') , optional:true, emit: junction
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script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def ignore_gtf = params.star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
def seq_platform = params.seq_platform ? "'PL:$params.seq_platform'" : ""
def seq_center = params.seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$params.seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform "
def out_sam_type = (options.args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted'
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def mv_unsorted_bam = (options.args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : ''
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"""
STAR \\
--genomeDir $index \\
--readFilesIn $reads \\
--runThreadN $task.cpus \\
--outFileNamePrefix $prefix. \\
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$out_sam_type \\
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$ignore_gtf \\
$seq_center \\
$options.args
$mv_unsorted_bam
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if [ -f ${prefix}.Unmapped.out.mate1 ]; then
mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq
gzip ${prefix}.unmapped_1.fastq
fi
if [ -f ${prefix}.Unmapped.out.mate2 ]; then
mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
gzip ${prefix}.unmapped_2.fastq
fi
STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt
"""
}