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https://github.com/MillironX/nf-core_modules.git
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3df4fe6085
* add freebayes/somatic and update freebayes/germline to new syntax and cram * add pytest * update with new freebayes/germline path
51 lines
2.2 KiB
Text
51 lines
2.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FREEBAYES_GERMLINE } from '../../../../modules/freebayes/germline/main.nf' addParams( options: [:] )
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workflow test_freebayes {
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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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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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targets = []
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samples = []
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populations = []
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cnv = []
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FREEBAYES_GERMLINE ( input, fasta, fai, targets, samples, populations, cnv)
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}
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workflow test_freebayes_bed {
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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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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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targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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samples = []
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populations = []
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cnv = []
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FREEBAYES_GERMLINE ( input, fasta, fai, targets, samples, populations, cnv)
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}
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workflow test_freebayes_cram {
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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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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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targets = []
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samples = []
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populations = []
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cnv = []
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FREEBAYES_GERMLINE ( input, fasta, fai, targets, samples, populations, cnv)
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}
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