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