mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
3ac21ff0dc
* Add abacas module * Add test for abacas module * Add Harshil to authorship * Updating test with the data uploaded to nf-core/datasets * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
45 lines
1.6 KiB
Text
45 lines
1.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process ABACAS {
|
|
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::abacas=1.3.1" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0"
|
|
} else {
|
|
container "quay.io/biocontainers/abacas:1.3.1--pl526_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(scaffold)
|
|
path fasta
|
|
|
|
output:
|
|
tuple val(meta), path('*.abacas*'), emit: results
|
|
path '*.version.txt' , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
abacas.pl \\
|
|
-r $fasta \\
|
|
-q $scaffold \\
|
|
$options.args \\
|
|
-o ${prefix}.abacas
|
|
|
|
mv nucmer.delta ${prefix}.abacas.nucmer.delta
|
|
mv nucmer.filtered.delta ${prefix}.abacas.nucmer.filtered.delta
|
|
mv nucmer.tiling ${prefix}.abacas.nucmer.tiling
|
|
mv unused_contigs.out ${prefix}.abacas.unused.contigs.out
|
|
echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|