nf-core_modules/modules/bwamem2/mem/main.nf
Matthieu Muffato 30b0485912
Added support for meta in bwamem2/index (#1921)
* Added support for meta in bwamem2/index

* Added missing description of the input meta map (fasta file)

* Made bwamem2/mem aware of the meta map the index carries

* The output meta map needs to be same as the input bam file

Don't merge it with the index's

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-07-26 21:48:47 +01:00

55 lines
1.8 KiB
Text

process BWAMEM2_MEM {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' :
'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' }"
input:
tuple val(meta), path(reads)
tuple val(meta2), 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 samtools_command = sort_bam ? 'sort' : 'view'
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
bwa-mem2 \\
mem \\
$args \\
-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
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}