nf-core_modules/modules/last/mafconvert/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process LAST_MAFCONVERT {
tag "$meta.id"
label 'process_high'
publishDir "${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::last=1250' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
} else {
container "quay.io/biocontainers/last:1250--h2e03b76_0"
}
input:
tuple val(meta), path(maf)
val(format)
output:
tuple val(meta), path("*.axt.gz"), optional:true, emit: axt_gz
tuple val(meta), path("*.blast.gz"), optional:true, emit: blast_gz
tuple val(meta), path("*.blasttab.gz"), optional:true, emit: blasttab_gz
tuple val(meta), path("*.chain.gz"), optional:true, emit: chain_gz
tuple val(meta), path("*.gff.gz"), optional:true, emit: gff_gz
tuple val(meta), path("*.html.gz"), optional:true, emit: html_gz
tuple val(meta), path("*.psl.gz"), optional:true, emit: psl_gz
tuple val(meta), path("*.sam.gz"), optional:true, emit: sam_gz
tuple val(meta), path("*.tab.gz"), optional:true, emit: tab_gz
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
maf-convert $options.args $format $maf | gzip --no-name \\
> ${prefix}.${format}.gz
# maf-convert has no --version option but lastdb (part of the same package) has.
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(lastdb --version 2>&1 | sed 's/lastdb //')
END_VERSIONS
"""
}