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45acc79667
* nf-core create * svdb merge module and test * remove to-do from test.yml * version * update meta.yml * mosdepth update * update md5sums * add stub * add stub * remove svdb * remove merge * Add tests * code linting fix * undo previous commit * revert code linting fix
36 lines
1.3 KiB
Text
36 lines
1.3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MOSDEPTH } from '../../../modules/mosdepth/main.nf'
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workflow test_mosdepth {
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input = [ [ id:'test', single_end:true ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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]
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MOSDEPTH ( input, [], [] )
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}
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workflow test_mosdepth_window {
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input = [ [ id:'test', single_end:true ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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]
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window = 100
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MOSDEPTH ( input, [], window )
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}
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workflow test_mosdepth_bed {
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input = [ [ id:'test', single_end:true ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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]
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bed = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
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MOSDEPTH ( input, bed, [] )
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}
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