nf-core_modules/software/bwameth/index/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process BWAMETH_INDEX {
tag "$fasta"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
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conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bwameth:0.20--py35_0"
} else {
container "quay.io/biocontainers/bwameth:0.20--py35_0"
}
input:
path fasta, stageAs: "bwameth/*"
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output:
path "bwameth" , emit: index
path "*.version.txt", emit: version
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script:
def software = getSoftwareName(task.process)
"""
bwameth.py index $fasta
echo \$(bwameth.py --version 2>&1) | cut -f2 -d" " > ${software}.version.txt
"""
}