mirror of
https://github.com/MillironX/nf-core_modules.git
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e8b33e6eb1
* hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Added genomecov scale module * Updated tagging * Removed extra module - began merging * Removed extra module tests * Updated genomecov to take a scale value * Updated line endings * Removed redundant test * Update tests/modules/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added checking for existing -bg arg * Update modules/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk> Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
57 lines
1.5 KiB
Text
57 lines
1.5 KiB
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_noscale {
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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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1
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]
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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_noscale {
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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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1
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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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workflow test_bedtools_genomecov_scale {
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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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0.5
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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_scale {
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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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0.5
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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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