nf-core_modules/modules/umitools/dedup/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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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process UMITOOLS_DEDUP {
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::umi_tools=1.1.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
} else {
container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
}
input:
tuple val(meta), path(bam), path(bai)
output:
tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path("*.tsv"), emit: tsv
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
umi_tools dedup \\
-I $bam \\
-S ${prefix}.bam \\
--output-stats=$prefix \\
$options.args \\
umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
"""
}