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f5d5926516
* Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
102 lines
4.4 KiB
Text
102 lines
4.4 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FREEBAYES } from '../../../modules/freebayes/main.nf'
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workflow test_freebayes {
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targets = []
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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[],
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[],
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targets
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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samples = []
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populations = []
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cnv = []
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FREEBAYES (input, fasta, fai, samples, populations, cnv)
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}
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workflow test_freebayes_bed {
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targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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[],
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[],
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targets
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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samples = []
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populations = []
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cnv = []
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FREEBAYES (input, fasta, fai, samples, populations, cnv)
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}
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workflow test_freebayes_cram {
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targets = []
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input = [ [ 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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[],
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[],
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targets
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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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samples = []
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populations = []
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cnv = []
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FREEBAYES (input, fasta, fai, samples, populations, cnv)
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}
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workflow test_freebayes_somatic {
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targets = []
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input = [ [ 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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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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targets
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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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samples = []
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populations = []
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cnv = []
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FREEBAYES (input, fasta, fai, samples, populations, cnv)
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}
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workflow test_freebayes_somatic_cram_intervals {
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targets = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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input = [ [ 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']['illumina']['test2_paired_end_sorted_cram'], 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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targets
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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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samples = []
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populations = []
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cnv = []
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FREEBAYES (input, fasta, fai, samples, populations, cnv)
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}
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