mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 12:43:09 +00:00
0745213729
* New last/mafconvert module to convert MAF alignments. The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5) format and converts them in another format (axt, blast, blasttab, chain, gff, html, psl, sam, tab). This new module is part of the work described in Issue #464. During this development, we fix the versiob of LAST to 1219 to ensure consistency. We will upgrade it later. * Delete white space. * Update the function.nf file to the dev version.
39 lines
1.5 KiB
Text
39 lines
1.5 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } 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=1219" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0"
|
|
} else {
|
|
container "quay.io/biocontainers/last:1219--h2e03b76_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(maf)
|
|
|
|
output:
|
|
tuple val(meta), path("*.{axt,blast,blasttab,chain,gff,html,psl,sam,tab}.gz"), emit: alm
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def format = params.options.format ? params.options.format : "tab"
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
zcat $maf | maf-convert $options.args $format | gzip --no-name \\
|
|
> ${prefix}.${format}.gz
|
|
|
|
# maf-convert has no --version option but lastdb (part of the same package) has.
|
|
echo \$(lastdb --version 2>&1) | sed 's/lastdb //' > ${software}.version.txt
|
|
"""
|
|
}
|