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979e57b7ac
* update tests * update * update * make the manta inputs consistant for germline/somatic/tumoronly * match chromosomes to cram file (chr21) * undo genotypegvfs * undo genotypegvfs * update manta input structure to match strelka. tuple(relevant input), path(fasta), path(fai) * update tests * fix typos * fix typos Co-authored-by: Smith Nicholas <smith@in.tum.de>
48 lines
2.4 KiB
Text
48 lines
2.4 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'
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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_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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[],[]
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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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MANTA_GERMLINE ( input, fasta, fai )
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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_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_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], 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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MANTA_GERMLINE ( input, fasta, fai )
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}
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workflow test_manta_germline_target_bed_jointcalling {
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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_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_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']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),],
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file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], 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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MANTA_GERMLINE ( input, fasta, fai )
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}
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