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98 lines
4.0 KiB
Plaintext
98 lines
4.0 KiB
Plaintext
process STAR_ALIGN {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' :
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'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }"
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input:
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tuple val(meta), path(reads)
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path index
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path gtf
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val star_ignore_sjdbgtf
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val seq_platform
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val seq_center
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output:
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tuple val(meta), path('*d.out.bam') , emit: bam
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tuple val(meta), path('*Log.final.out') , emit: log_final
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tuple val(meta), path('*Log.out') , emit: log_out
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tuple val(meta), path('*Log.progress.out'), emit: log_progress
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path "versions.yml" , emit: versions
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tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted
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tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript
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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
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tuple val(meta), path('*.tab') , optional:true, emit: tab
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tuple val(meta), path('*.out.junction') , optional:true, emit: junction
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tuple val(meta), path('*.out.sam') , optional:true, emit: sam
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def ignore_gtf = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
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def seq_platform = seq_platform ? "'PL:$seq_platform'" : ""
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def seq_center = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform "
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def out_sam_type = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted'
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def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : ''
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"""
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STAR \\
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--genomeDir $index \\
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--readFilesIn $reads \\
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--runThreadN $task.cpus \\
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--outFileNamePrefix $prefix. \\
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$out_sam_type \\
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$ignore_gtf \\
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$seq_center \\
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$args
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$mv_unsorted_bam
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if [ -f ${prefix}.Unmapped.out.mate1 ]; then
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mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq
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gzip ${prefix}.unmapped_1.fastq
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fi
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if [ -f ${prefix}.Unmapped.out.mate2 ]; then
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mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
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gzip ${prefix}.unmapped_2.fastq
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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star: \$(STAR --version | sed -e "s/STAR_//g")
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}Xd.out.bam
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touch ${prefix}.Log.final.out
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touch ${prefix}.Log.out
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touch ${prefix}.Log.progress.out
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touch ${prefix}.sortedByCoord.out.bam
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touch ${prefix}.toTranscriptome.out.bam
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touch ${prefix}.Aligned.unsort.out.bam
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touch ${prefix}.unmapped_1.fastq.gz
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touch ${prefix}.unmapped_2.fastq.gz
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touch ${prefix}.tab
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touch ${prefix}.Chimeric.out.junction
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touch ${prefix}.out.sam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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star: \$(STAR --version | sed -e "s/STAR_//g")
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
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END_VERSIONS
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"""
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}
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