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* mutect2 files added, first draft of module code entered * removing comment from main.nf * removing comment from main.nf * test added, commit made before editing yaml * tests added, still needs final check and info/comments added * gatk4 version changed to gatk4=4.2.0.0 * multiple sample support added, information added to module yaml file * Update meta.yml fixed linting error * add keywords to meta.yml * Corrections made to meta.yml * removed whitespace from meta.yml Co-authored-by: Gavin.Mackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
62 lines
4.1 KiB
Text
62 lines
4.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_MUTECT2 } from '../../../../modules/gatk4/mutect2/main.nf' addParams( options: [:] )
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workflow test_gatk4_mutect2_tumor_normal_pair {
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input = [ [ id:'test'], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) , file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) , file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
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["testN"]
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]
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run_single = false
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run_pon = false
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fastaidx = 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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germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
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germline_resource_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
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panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
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panel_of_normals_idx = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
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GATK4_MUTECT2 ( input , run_single , run_pon , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx )
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}
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workflow test_gatk4_mutect2_tumor_single {
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input = [ [ id:'test'], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
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[ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
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[]
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]
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run_single = true
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run_pon = false
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fastaidx = 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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germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
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germline_resource_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
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panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
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panel_of_normals_idx = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
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GATK4_MUTECT2 ( input , run_single , run_pon , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx )
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}
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workflow test_gatk4_mutect2_generate_pon {
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input = [ [ id:'test'], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
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[]
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]
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run_single = false
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run_pon = true
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fastaidx = 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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germline_resource = []
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germline_resource_idx = []
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panel_of_normals = []
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panel_of_normals_idx = []
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GATK4_MUTECT2 ( input , run_single , run_pon , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx )
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}
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