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5d8edefb26
* new module gatk4/printsvevidence * linting Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
116 lines
3.7 KiB
Text
116 lines
3.7 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_PE } from '../../../../modules/gatk4/printsvevidence/main.nf'
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include { GATK4_PRINTSVEVIDENCE as GATK4_PRINTSVEVIDENCE_SR } from '../../../../modules/gatk4/printsvevidence/main.nf'
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include { GATK4_COLLECTSVEVIDENCE } from '../../../../modules/gatk4/collectsvevidence/main.nf'
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workflow test_gatk4_printsvevidence {
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input = Channel.of(
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[
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[ id:'normal', 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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],
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[
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[ id:'tumour', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true),
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[],
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[]
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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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fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_COLLECTSVEVIDENCE(
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input,
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fasta,
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fasta_fai,
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dict
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)
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pe_files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence
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.combine(GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index, by:0)
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sr_files = GATK4_COLLECTSVEVIDENCE.out.split_read_evidence
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.combine(GATK4_COLLECTSVEVIDENCE.out.split_read_evidence_index, by:0)
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GATK4_PRINTSVEVIDENCE_PE(
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pe_files,
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[],
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fasta,
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fasta_fai,
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dict
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)
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GATK4_PRINTSVEVIDENCE_SR(
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sr_files,
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[],
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fasta,
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fasta_fai,
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dict
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)
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}
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workflow test_gatk4_printsvevidence_bed_no_fasta {
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input = Channel.of(
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[
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[ id:'normal', 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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],
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[
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[ id:'tumour', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true),
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[],
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[]
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]
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)
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fasta = []
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fasta_fai = []
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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GATK4_COLLECTSVEVIDENCE(
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input,
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fasta,
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fasta_fai,
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dict
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)
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pe_files = GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence
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.combine(GATK4_COLLECTSVEVIDENCE.out.paired_end_evidence_index, by:0)
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sr_files = GATK4_COLLECTSVEVIDENCE.out.split_read_evidence
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.combine(GATK4_COLLECTSVEVIDENCE.out.split_read_evidence_index, by:0)
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GATK4_PRINTSVEVIDENCE_PE(
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pe_files,
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bed,
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fasta,
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fasta_fai,
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dict
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)
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GATK4_PRINTSVEVIDENCE_SR(
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sr_files,
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bed,
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fasta,
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fasta_fai,
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dict
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)
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}
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