nf-core_modules/software/pairtools/select/main.nf
JIANHONG OU e0b7952b56
Pairtools select (#523)
* add software/pairtools

* create a branch for pairtools/select

* fix the different output of conda and docker.

* rmove the md5sum for gzip files.

* Update software/pairtools/select/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* update test file and documentation.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-06-23 15:58:31 +02:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PAIRTOOLS_SELECT {
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::pairtools=0.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5"
} else {
container "quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5"
}
input:
tuple val(meta), path(input)
output:
tuple val(meta), path("*.selected.pairs.gz") , emit: selected
tuple val(meta), path("*.unselected.pairs.gz"), emit: unselected
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
pairtools select \\
"$options.args" \\
-o ${prefix}.selected.pairs.gz \\
--output-rest ${prefix}.unselected.pairs.gz \\
${input}
echo \$(pairtools --version 2>&1) | sed 's/pairtools.*version //' > ${software}.version.txt
"""
}