nf-core_modules/software/genmap/mappability/main.nf
JIANHONG OU 18440df87a
add genmap/mappability (#509)
* 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>
2021-05-25 22:12:10 +01:00

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1.3 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GENMAP_MAPPABILITY {
tag '$fasta'
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], 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 index
output:
path "*.wig" , optional:true, emit: wig
path "*.bedgraph" , optional:true, emit: bedgraph
path "*.txt" , optional:true, emit: txt
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
genmap \\
map \\
$options.args \\
-I $index \\
-O mappability
echo \$(genmap --version 2>&1) | sed 's/GenMap version: //; s/SeqAn.*\$//' > ${software}.version.txt
"""
}