mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
18440df87a
* add genmap/mappability * Add index module. Remove -w parameter from mappability module. * change the output of genmap/index * fix the lint error which can not handle stageAs. * Apply suggestions from code review * Update main.nf * Update test.yml * Update main.nf * Update test.yml * Update tests/software/genmap/mappability/main.nf * Update software/genmap/mappability/main.nf * Update software/genmap/mappability/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
38 lines
1.1 KiB
Text
38 lines
1.1 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process GENMAP_INDEX {
|
|
tag '$fasta'
|
|
label 'process_high'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
|
|
|
|
conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1"
|
|
} else {
|
|
container "quay.io/biocontainers/genmap:1.3.0--h1b792b2_1"
|
|
}
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path "genmap" , emit: index
|
|
path "*.version.txt", emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
"""
|
|
genmap \\
|
|
index \\
|
|
-F $fasta \\
|
|
-I genmap
|
|
|
|
echo \$(genmap --version 2>&1) | sed 's/GenMap version: //; s/SeqAn.*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|