nf-core_modules/modules/bwa/sampe/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

42 lines
1.4 KiB
Text

process BWA_SAMPE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' :
'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' }"
input:
tuple val(meta), path(reads), path(sai)
path index
output:
tuple val(meta), path("*.bam"), emit: bam
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def read_group = meta.read_group ? "-r ${meta.read_group}" : ""
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
bwa sampe \\
$args \\
$read_group \\
\$INDEX \\
$sai \\
$reads | samtools sort -@ ${task.cpus - 1} -O bam - > ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}