From 3a4e415fe21982ccb39807d71c16e7d6ad0a1c1a Mon Sep 17 00:00:00 2001 From: Lucpen Date: Mon, 2 May 2022 13:30:18 +0200 Subject: [PATCH] chores adding dummy files for stubs --- tests/modules/gatk4/mutect2/main.nf | 18 +++++++++--------- tests/modules/gatk4/revertsam/main.nf | 2 +- tests/modules/gatk4/samtofastq/main.nf | 2 +- tests/modules/samtools/view/main.nf | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/tests/modules/gatk4/mutect2/main.nf b/tests/modules/gatk4/mutect2/main.nf index 619d28b8..251e1987 100644 --- a/tests/modules/gatk4/mutect2/main.nf +++ b/tests/modules/gatk4/mutect2/main.nf @@ -121,18 +121,18 @@ workflow test_gatk4_mutect2_mitochondria { workflow test_gatk4_mutect2_tumor_single_stubs { input = [ [ id:'test'], // meta map - [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)], - [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)], + [ "foo.bam" ], + [ "foo.bam.bai" ], [] ] - 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) - germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) - germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) - panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) - panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) + fasta = "genome.fasta" + fai = "genome.fasta.fai" + dict = "genome.fasta.dict" + germline_resource = "genome_gnomAD.r2.1.1.vcf.gz" + germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi" + panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz" + panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi" GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) } diff --git a/tests/modules/gatk4/revertsam/main.nf b/tests/modules/gatk4/revertsam/main.nf index 5b14d471..738ecd8f 100644 --- a/tests/modules/gatk4/revertsam/main.nf +++ b/tests/modules/gatk4/revertsam/main.nf @@ -14,7 +14,7 @@ workflow test_gatk4_revertsam { workflow test_gatk4_revertsam_stubs { input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + "foo_paired_end.bam" ] GATK4_REVERTSAM ( input ) diff --git a/tests/modules/gatk4/samtofastq/main.nf b/tests/modules/gatk4/samtofastq/main.nf index aad80057..79d04c7c 100644 --- a/tests/modules/gatk4/samtofastq/main.nf +++ b/tests/modules/gatk4/samtofastq/main.nf @@ -22,7 +22,7 @@ workflow test_gatk4_samtofastq_paired_end { workflow test_gatk4_samtofastq_paired_end_stubs { input = [ [ id:'test', single_end: false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ] + [ "foo_paired_end.bam" ] ] GATK4_SAMTOFASTQ ( input ) diff --git a/tests/modules/samtools/view/main.nf b/tests/modules/samtools/view/main.nf index 0e3f597e..bdad1078 100644 --- a/tests/modules/samtools/view/main.nf +++ b/tests/modules/samtools/view/main.nf @@ -25,7 +25,7 @@ workflow test_samtools_view_cram { workflow test_samtools_view_stubs { input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), + "foo_paired_end.bam", [] ]