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56 lines
2 KiB
Text
56 lines
2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SVTK_STANDARDIZE } from '../../../../modules/svtk/standardize/main.nf'
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include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
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workflow test_svtk_standardize {
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input = [
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[ 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_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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fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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MANTA_GERMLINE(
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input,
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fasta,
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fasta_fai
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)
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SVTK_STANDARDIZE (
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MANTA_GERMLINE.out.diploid_sv_vcf,
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fasta_fai
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)
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}
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workflow test_svtk_standardize_no_contigs {
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input = [
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[ 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_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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fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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MANTA_GERMLINE(
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input,
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fasta,
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fasta_fai
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)
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SVTK_STANDARDIZE (
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MANTA_GERMLINE.out.diploid_sv_vcf,
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[]
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)
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}
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