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* initial commit to setup branch * workflow finished * Update nextflow.config * tumour to tumor, getpileup passed as nomral and tumor * paired_somatic renamed to tumor_normal_somatic * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * updated index names in meta.yml * changed index file names in main script and test * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Apply suggestions from code review * fixed bug from changes * Apply suggestions from code review * modified yml to allow new subworkflow testing * Update test.yml * Update test.yml * add applyvqsr * added memory options, new test data used * Update main.nf * Update main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
41 lines
2.3 KiB
Text
41 lines
2.3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_APPLYVQSR } from '../../../../modules/gatk4/applyvqsr/main.nf'
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workflow test_gatk4_applyvqsr {
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input = [ [ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_recal'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_recal_idx'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_tranches'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
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allelespecific = false
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truthsensitivity = '99.0'
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mode = 'SNP'
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GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode )
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}
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workflow test_gatk4_applyvqsr_allele_specific {
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input = [ [ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal_idx'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_tranches'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
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allelespecific = true
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truthsensitivity = '99.0'
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mode = 'SNP'
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GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode )
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}
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