nf-core_modules/modules/bandage/image/main.nf

39 lines
1.4 KiB
Text
Raw Normal View History

2021-02-04 01:31:58 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
2021-02-04 01:31:58 +00:00
process BANDAGE_IMAGE {
tag "${meta.id}"
label 'process_low'
publishDir "${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']) }
2021-02-04 01:31:58 +00:00
2021-02-16 23:58:23 +00:00
conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null)
2021-02-04 01:31:58 +00:00
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2"
} else {
container "quay.io/biocontainers/bandage:0.8.1--hc9558a2_2"
}
input:
tuple val(meta), path(gfa)
2021-02-04 01:34:25 +00:00
2021-02-04 01:31:58 +00:00
output:
tuple val(meta), path('*.png'), emit: png
tuple val(meta), path('*.svg'), emit: svg
path '*.version.txt' , emit: version
2021-02-04 01:34:25 +00:00
2021-02-04 01:31:58 +00:00
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
Bandage image $gfa ${prefix}.png $options.args
Bandage image $gfa ${prefix}.svg $options.args
2021-02-04 01:34:25 +00:00
2021-02-04 01:31:58 +00:00
echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//' > ${software}.version.txt
"""
}