mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 12:43:09 +00:00
7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
49 lines
2.1 KiB
Text
49 lines
2.1 KiB
Text
// 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
|
|
"""
|
|
}
|