nf-core_modules/modules/bowtie/align/main.nf
FriederikeHanssen 897c33d5da
Samtools version update (#1507)
* Fix typo

* update version to 1.15.1

* Fix md5sums

* update mulled containers

* update md5sums

* update md5sums
2022-04-11 14:26:28 +02:00

56 lines
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Text

process BOWTIE_ALIGN {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' :
'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-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
"""
}