nf-core_modules/modules/bwamem2/mem/main.nf
FriederikeHanssen 950700bcdc
Update samtools version (#1361)
* Update samtools version

* update checksums
2022-02-28 23:13:11 +01:00

46 lines
1.5 KiB
Text

process BWAMEM2_MEM {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' :
'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' }"
input:
tuple val(meta), path(reads)
path index
val sort_bam
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 args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
def samtools_command = sort_bam ? 'sort' : 'view'
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
bwa-mem2 \\
mem \\
$args \\
$read_group \\
-t $task.cpus \\
\$INDEX \\
$reads \\
| samtools $samtools_command $args2 -@ $task.cpus -o ${prefix}.bam -
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}