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

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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
"""
}