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* Add atlas/call * Apply suggestions from code review * Update modules/atlas/call/main.nf Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com> * Apply suggestions from code review Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>
22 lines
823 B
Text
22 lines
823 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ATLAS_CALL } from '../../../../modules/atlas/call/main.nf'
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workflow test_atlas_call {
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input = [
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[ 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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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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recal = []
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pmd = []
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known_alleles = []
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method = 'randomBase'
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ATLAS_CALL ( input, fasta, fai, recal, pmd, known_alleles, method )
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}
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