nf-core_modules/modules/bwa/samse/main.nf
2022-02-04 09:53:32 +01:00

42 lines
1.4 KiB
Text

process BWA_SAMSE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' :
'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }"
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 samse \\
$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
"""
}