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1287ba48fe
* Update version & add intervals usage * Fix config when passing intervals as file * Use proper paths
36 lines
1.7 KiB
Text
36 lines
1.7 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { DEEPVARIANT } from '../../../modules/deepvariant/main.nf'
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include { DEEPVARIANT as DEEPVARIANT_INTERVALS } from '../../../modules/deepvariant/main.nf'
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workflow test_deepvariant {
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bam_tuple_ch = Channel.of([ [ id:'test', single_end:false ], // 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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[]
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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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DEEPVARIANT ( bam_tuple_ch, fasta, fai)
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}
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workflow test_deepvariant_cram_intervals {
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cram_tuple_ch = Channel.of([[ 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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file(params.test_data['homo_sapiens']['genome']['genome_bed'], 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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DEEPVARIANT_INTERVALS ( cram_tuple_ch, fasta, fai)
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}
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