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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
29 lines
814 B
Text
29 lines
814 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BEDTOOLS_GENOMECOV } from '../../../../modules/bedtools/genomecov/main.nf' addParams( options: [suffix: '_out'] )
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workflow test_bedtools_genomecov {
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input = [
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[ id:'test'],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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sizes = file('dummy_chromosome_sizes')
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extension = 'txt'
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BEDTOOLS_GENOMECOV ( input, sizes, extension )
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}
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workflow test_bedtools_genomecov_nonbam {
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input = [
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[ id:'test'],
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file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
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]
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sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
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extension = 'txt'
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BEDTOOLS_GENOMECOV ( input, sizes, extension )
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}
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