nf-core_modules/modules/hmmcopy/gccounter/main.nf
Simon Pearce cac6dc83bb
gccounter module for hmmcopy (#1003)
* hmmcopy gccounter working

* Update modules/hmmcopy/gccounter/main.nf

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>

* Update main.nf

Changed version to 0.1.1 as the container says

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-02 09:59:25 +00:00

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1.2 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
def VERSION = '0.1.1'
process HMMCOPY_GCCOUNTER {
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_5"
} else {
container "quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_5"
}
input:
path fasta
output:
path "*.gc.wig" , emit: wig
path "versions.yml", emit: versions
script:
"""
gcCounter \\
$options.args \\
${fasta} > ${fasta.baseName}.gc.wig
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo $VERSION)
END_VERSIONS
"""
}