2020-12-17 23:50:24 +00:00
|
|
|
// Import generic module functions
|
|
|
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
|
|
|
|
|
|
params.options = [:]
|
|
|
|
|
def options = initOptions(params.options)
|
|
|
|
|
|
|
|
|
|
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), publish_id:meta.id) }
|
|
|
|
|
|
|
|
|
|
// Note: 2.7X indices incompatible with AWS iGenomes.
|
|
|
|
|
conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
|
|
|
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
|
|
|
container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
|
|
|
|
|
} else {
|
|
|
|
|
container "quay.io/biocontainers/star:2.6.1d--0"
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
input:
|
|
|
|
|
tuple val(meta), path(reads)
|
|
|
|
|
path index
|
|
|
|
|
path gtf
|
|
|
|
|
|
|
|
|
|
output:
|
|
|
|
|
tuple val(meta), path("*Aligned.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 "*.version.txt" , emit: version
|
|
|
|
|
|
|
|
|
|
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("*fastq.gz") , optional:true, emit: fastq
|
|
|
|
|
tuple val(meta), path("*.tab") , optional:true, emit: tab
|
|
|
|
|
|
|
|
|
|
script:
|
|
|
|
|
def software = getSoftwareName(task.process)
|
|
|
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
|
|
|
def ignore_gtf = params.star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
|
|
|
|
|
def seq_center = params.seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$params.seq_center' 'SM:$prefix'" : "--outSAMattrRGline ID:$prefix 'SM:$prefix'"
|
|
|
|
|
"""
|
|
|
|
|
STAR \\
|
|
|
|
|
--genomeDir $index \\
|
|
|
|
|
--readFilesIn $reads \\
|
|
|
|
|
--runThreadN $task.cpus \\
|
|
|
|
|
--outFileNamePrefix $prefix. \\
|
|
|
|
|
$ignore_gtf \\
|
|
|
|
|
$seq_center \\
|
|
|
|
|
$options.args
|
|
|
|
|
|
|
|
|
|
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
|
|
|
|
|
"""
|
|
|
|
|
}
|
