nf-core_modules/tests/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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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GENMAP_INDEX } from '../../../../software/genmap/index/main.nf' addParams( options: [:] )
include { GENMAP_MAPPABILITY } from '../../../../software/genmap/mappability/main.nf' addParams( options: [args : '-K 50 -E 2 -w -t -bg'] )
workflow test_genmap_map {
input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
GENMAP_INDEX ( input )
GENMAP_MAPPABILITY ( GENMAP_INDEX.out.index )
}