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a813e2e3a6
* local tests and linting passing (#585) * fix: picard filtersamreads input (#610) * Move readlist into same input channel as bam * Update test reflecting input restructuring * Update tests/modules/picard/filtersamreads/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix test Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added module arriba (#611) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml * Added module arriba * Changes in test configs * Added module Arriba for fusion detection * Fixed review comments * Added an output option for discarded fusions * Resolved some conflits * conflicts * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * added test for new header * enhance module fastp: add `save_merged` (#598) (#614) * enhance module fastp: add `save_merged` (#598) * removed md5sum checks from log and json * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
40 lines
1.3 KiB
Text
40 lines
1.3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BCFTOOLS_REHEADER } from '../../../../modules/bcftools/reheader/main.nf' addParams( options: [suffix: '.updated'] )
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workflow test_bcftools_reheader_update_sequences {
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input = [
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[ id:'test', single_end:false ],
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
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]
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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header = []
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BCFTOOLS_REHEADER ( input, fai, header )
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}
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workflow test_bcftools_reheader_new_header {
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input = [
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[ id:'test', single_end:false ],
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
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]
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fai = []
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header = file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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BCFTOOLS_REHEADER ( input, fai, header )
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}
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workflow test_bcftools_reheader_new_header_update_sequences {
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input = [
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[ id:'test', single_end:false ],
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
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]
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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header = file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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BCFTOOLS_REHEADER ( input, fai, header )
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}
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