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80d8e87fa4
* feat: all manta/single to modules * fix module name * fix module name * fix: changes from review comments * fix: test data
35 lines
1.6 KiB
Text
35 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf' addParams( options: [:] )
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workflow test_manta_germline {
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input = [
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[ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], 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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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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bed = []
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bed_tbi = []
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MANTA_GERMLINE ( input, fasta, fai, bed, bed_tbi )
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}
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workflow test_manta_germline_target_bed {
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input = [
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[ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], 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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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
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bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
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MANTA_GERMLINE ( input, fasta, fai, bed, bed_tbi )
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}
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