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754db250a0
* remove params statement * add manta/somatic module * fix strelka target bed thing * removing checksums should make this pass * Update modules/manta/somatic/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix indentation Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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 { STRELKA_GERMLINE } from '../../../../modules/strelka/germline/main.nf' addParams( options: [:] )
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workflow test_strelka_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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target_bed = []
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target_bed_tbi = []
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STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi )
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}
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workflow test_strelka_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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target_bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
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target_bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
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STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi )
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}
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