mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
72 lines
2.9 KiB
Text
72 lines
2.9 KiB
Text
process STAR_ALIGN {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
|
|
// Note: 2.7X indices incompatible with AWS iGenomes.
|
|
conda (params.enable_conda ? 'bioconda::star=2.7.9a' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/star:2.7.9a--h9ee0642_0' :
|
|
'quay.io/biocontainers/star:2.7.9a--h9ee0642_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
path index
|
|
path gtf
|
|
val star_ignore_sjdbgtf
|
|
val seq_platform
|
|
val seq_center
|
|
|
|
output:
|
|
tuple val(meta), path('*d.out.bam') , emit: bam
|
|
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 "versions.yml" , emit: versions
|
|
|
|
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
|
|
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
|
|
tuple val(meta), path('*.out.sam') , optional:true, emit: sam
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def ignore_gtf = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
|
|
def seq_platform = seq_platform ? "'PL:$seq_platform'" : ""
|
|
def seq_center = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform "
|
|
def out_sam_type = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted'
|
|
def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : ''
|
|
"""
|
|
STAR \\
|
|
--genomeDir $index \\
|
|
--readFilesIn $reads \\
|
|
--runThreadN $task.cpus \\
|
|
--outFileNamePrefix $prefix. \\
|
|
$out_sam_type \\
|
|
$ignore_gtf \\
|
|
$seq_center \\
|
|
$args
|
|
|
|
$mv_unsorted_bam
|
|
|
|
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 ${prefix}.unmapped_2.fastq
|
|
fi
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
star: \$(STAR --version | sed -e "s/STAR_//g")
|
|
END_VERSIONS
|
|
"""
|
|
}
|