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4619d012e5
* Add CRAM support to allelecounter * Update meta.yml * Rename bam,bai to input,input_index * Apply suggestions from code review * Fix reference to renamed variable Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
26 lines
1.2 KiB
Text
26 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ALLELECOUNTER } from '../../../modules/allelecounter/main.nf' addParams( options: [:] )
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workflow test_allelecounter_bam {
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input = [ [ id:'test', single_end:false ], // meta map
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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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positions = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
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ALLELECOUNTER ( input, positions, [] )
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}
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workflow test_allelecounter_cram {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
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]
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positions = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
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fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
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ALLELECOUNTER ( input, positions, fasta )
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}
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