nf-core_modules/modules/dshbio/exportsegments/main.nf
Michael L Heuer b50f4e3d59
Update dsh-bio to 2.0.6. (#1075)
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-16 11:37:27 +00:00

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1.4 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process DSHBIO_EXPORTSEGMENTS {
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::dsh-bio=2.0.6" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0"
} else {
container "quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0"
}
input:
tuple val(meta), path(gfa)
output:
tuple val(meta), path("*.fa"), emit: fasta
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
dsh-bio \\
export-segments \\
$options.args \\
-i $gfa \\
-o ${prefix}.fa
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(dsh-bio --version 2>&1 | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ')
END_VERSIONS
"""
}