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39 lines
1.7 KiB
Text
39 lines
1.7 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf'
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include { BISCUIT_PILEUP } from '../../../../modules/biscuit/pileup/main.nf'
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workflow test_biscuit_pileup {
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input = [ [ id:'test' ], // meta map
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[file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)],
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[file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)],
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[], //tumor bam
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[] //tumor bai
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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BISCUIT_INDEX ( fasta )
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BISCUIT_PILEUP ( input, BISCUIT_INDEX.out.index )
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}
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workflow test_biscuit_pileup_somatic {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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BISCUIT_INDEX ( fasta )
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BISCUIT_PILEUP ( input, BISCUIT_INDEX.out.index )
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}
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