nf-core_modules/modules/bwa/mem/main.nf
Harshil Patel e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* Update README

* Rename pytest_software.yml to pytest_modules.yml

* Rename main software directory to modules

* Remove deprecated modules

* Rename tests software to modules

* Replace paths for tests in pytest_modules.yml

* Replace software with modules in Github Actions

* Replace software with modules in main.nf tests

* Rename software to modules in test.yml
2021-07-07 10:10:18 +01:00

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1.7 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process BWA_MEM {
tag "$meta.id"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
} else {
container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
}
input:
tuple val(meta), path(reads)
path index
output:
tuple val(meta), path("*.bam"), emit: bam
path "*.version.txt" , emit: version
script:
def split_cpus = Math.floor(task.cpus/2)
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
bwa mem \\
$options.args \\
$read_group \\
-t ${split_cpus} \\
\$INDEX \\
$reads \\
| samtools view $options.args2 -@ ${split_cpus} -bhS -o ${prefix}.bam -
echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
"""
}