nf-core_modules/modules/preseq/lcextrap/main.nf
Gregor Sturm 906577873b
Bulk update modules to use versions.yml (#739)
* New functions.nf

* Convert code to create versions.yml

* Update meta.yml

* update output channel

* Fix more meta.yml

* Manually update remaining modules

* remove superflous echo

* Fix misformatted meta.yml files

* Fix yaml, was list instead of dict

* fix version for bcftools

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 09:41:24 +01:00

48 lines
1.6 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PRESEQ_LCEXTRAP {
tag "$meta.id"
label 'process_medium'
label 'error_ignore'
publishDir "${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::preseq=3.1.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/preseq:3.1.2--h06ef8b0_1"
} else {
container "quay.io/biocontainers/preseq:3.1.2--h06ef8b0_1"
}
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.ccurve.txt"), emit: ccurve
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def paired_end = meta.single_end ? '' : '-pe'
"""
preseq \\
lc_extrap \\
$options.args \\
$paired_end \\
-output ${prefix}.ccurve.txt \\
$bam
cp .command.err ${prefix}.command.log
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(preseq 2>&1 | sed 's/^.*Version: //; s/Usage:.*\$//')
END_VERSIONS
"""
}