mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
56 lines
2 KiB
Text
56 lines
2 KiB
Text
process BOWTIE_ALIGN {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.11' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0' :
|
|
'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
path index
|
|
|
|
output:
|
|
tuple val(meta), path('*.bam'), emit: bam
|
|
tuple val(meta), path('*.out'), emit: log
|
|
path "versions.yml" , emit: versions
|
|
tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def args2 = task.ext.args2 ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : ''
|
|
def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}"
|
|
"""
|
|
INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'`
|
|
bowtie \\
|
|
--threads $task.cpus \\
|
|
--sam \\
|
|
-x \$INDEX \\
|
|
-q \\
|
|
$unaligned \\
|
|
$args \\
|
|
$endedness \\
|
|
2> ${prefix}.out \\
|
|
| samtools view $args2 -@ $task.cpus -bS -o ${prefix}.bam -
|
|
|
|
if [ -f ${prefix}.unmapped.fastq ]; then
|
|
gzip ${prefix}.unmapped.fastq
|
|
fi
|
|
if [ -f ${prefix}.unmapped_1.fastq ]; then
|
|
gzip ${prefix}.unmapped_1.fastq
|
|
gzip ${prefix}.unmapped_2.fastq
|
|
fi
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
bowtie: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
|
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|