From cd60b4c6eb0ecee7dbcaa2e404336545b4b6ecee Mon Sep 17 00:00:00 2001 From: Rike Date: Sun, 22 May 2022 13:35:35 +0200 Subject: [PATCH] add in testdata paths --- .../gatk4/filtervarianttranches/main.nf | 38 +++++++------------ .../filtervarianttranches/nextflow.config | 5 ++- 2 files changed, 16 insertions(+), 27 deletions(-) diff --git a/tests/modules/gatk4/filtervarianttranches/main.nf b/tests/modules/gatk4/filtervarianttranches/main.nf index 650e78a8..91dde3d4 100644 --- a/tests/modules/gatk4/filtervarianttranches/main.nf +++ b/tests/modules/gatk4/filtervarianttranches/main.nf @@ -3,36 +3,24 @@ nextflow.enable.dsl = 2 include { GATK4_FILTERVARIANTTRANCHES } from '../../../../modules/gatk4/filtervarianttranches/main.nf' - +include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/gatk4/cnnscorevariants/main.nf' +include { GATK4_HAPLOTYPECALLER } from '../../../../modules/gatk4/haplotypecaller/main.nf' workflow test_gatk4_filtervarianttranches { + resources = [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] + resources_index = [ + file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true), + ] + input = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true), [] ] - resources = [ - file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), - //file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true), - //file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true), - //file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true) - ] - resources_index =[ file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true), - //file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true), - //file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true), - //file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true) - ] - // , [ - // 'hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz', - // 'omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz', - // '1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz', - // 'dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' - // ]] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - - GATK4_FILTERVARIANTTRANCHES ( input, resources, resources_index, fasta, fai, dict) + GATK4_FILTERVARIANTTRANCHES (input , resources, resources_index, fasta, fai, dict) } diff --git a/tests/modules/gatk4/filtervarianttranches/nextflow.config b/tests/modules/gatk4/filtervarianttranches/nextflow.config index 50f50a7a..7a8f0a06 100644 --- a/tests/modules/gatk4/filtervarianttranches/nextflow.config +++ b/tests/modules/gatk4/filtervarianttranches/nextflow.config @@ -1,5 +1,6 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file + + ext.args = "--info-key CNN_1D" +}