nf-core_modules/modules/bwa/aln/main.nf
James A. Fellows Yates ab93a1afa7
update: BWA/ALN (#653)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Remove reads from output channel following module guidelines. Should do a .join() based on $meta, to reassociate.

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-17 15:55:54 +02:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process BWA_ALN {
tag "$meta.id"
label 'process_medium'
publishDir "${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" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--h5bf99c6_8"
} else {
container "quay.io/biocontainers/bwa:0.7.17--h5bf99c6_8"
}
input:
tuple val(meta), path(reads)
path index
output:
tuple val(meta), path("*.sai"), emit: sai
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
bwa aln \\
$options.args \\
-t $task.cpus \\
-f ${prefix}.sai \\
\$INDEX \\
${reads}
echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
"""
} else {
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
bwa aln \\
$options.args \\
-t $task.cpus \\
-f ${prefix}.1.sai \\
\$INDEX \\
${reads[0]}
bwa aln \\
$options.args \\
-t $task.cpus \\
-f ${prefix}.2.sai \\
\$INDEX \\
${reads[1]}
echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
"""
}
}