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29 lines
1.3 KiB
Text
29 lines
1.3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PICARD_COLLECTHSMETRICS } from '../../../../modules/picard/collecthsmetrics/main.nf'
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workflow test_picard_collecthsmetrics {
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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_bam'], checkIfExists: true) ]
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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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bait_intervals = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
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target_intervals = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
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PICARD_COLLECTHSMETRICS ( input, fasta, fai, bait_intervals, target_intervals )
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}
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workflow test_picard_collecthsmetrics_nofasta {
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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_bam'], checkIfExists: true) ]
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bait_intervals = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
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target_intervals = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
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PICARD_COLLECTHSMETRICS ( input, [], [], bait_intervals, target_intervals )
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}
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