From 612995c0e60049ecd14e573878ef3fef132128e4 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 26 Feb 2024 14:23:01 +0000 Subject: [PATCH] Using params.modules_testdata_base_path instead of params.test_data --- .../gatk4/baserecalibrator/tests/main.nf.test | 62 +++++++++---------- .../baserecalibrator/tests/main.nf.test.snap | 40 ++++++------ 2 files changed, 51 insertions(+), 51 deletions(-) diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test index 1262b694411f..fbd91beae2b4 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test @@ -15,15 +15,15 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - input[4] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) - input[5] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) """ } @@ -45,15 +45,15 @@ nextflow_process { input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - input[4] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) - input[5] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) """ } @@ -75,20 +75,20 @@ nextflow_process { input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) input[4] = [ - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) ] input[5] = [ - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] """ @@ -141,15 +141,15 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [] ] - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - input[4] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) - input[5] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) """ } } diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap index 8291304ba870..8848eff699c8 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.recal.table:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -18,7 +18,7 @@ { "id": "test" }, - "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.recal.table:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -28,9 +28,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "24.01.0" }, - "timestamp": "2024-02-13T16:16:00.04396" + "timestamp": "2024-02-26T07:59:09.802474612" }, "sarscov2 - bam - intervals": { "content": [ @@ -40,7 +40,7 @@ { "id": "test" }, - "test.table:md5,9ecb5f00a2229291705addc09c0ec231" + "test.recal.table:md5,9ecb5f00a2229291705addc09c0ec231" ] ], "1": [ @@ -51,7 +51,7 @@ { "id": "test" }, - "test.table:md5,9ecb5f00a2229291705addc09c0ec231" + "test.recal.table:md5,9ecb5f00a2229291705addc09c0ec231" ] ], "versions": [ @@ -61,9 +61,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "24.01.0" }, - "timestamp": "2024-02-13T16:15:17.899391" + "timestamp": "2024-02-26T07:58:46.088383653" }, "sarscov2 - bam - multiple sites": { "content": [ @@ -73,7 +73,7 @@ { "id": "test" }, - "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + "test.recal.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" ] ], "1": [ @@ -84,7 +84,7 @@ { "id": "test" }, - "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + "test.recal.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" ] ], "versions": [ @@ -94,9 +94,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "24.01.0" }, - "timestamp": "2024-02-13T16:15:47.770383" + "timestamp": "2024-02-26T07:59:00.753963509" }, "homo_sapiens - cram ": { "content": [ @@ -106,7 +106,7 @@ { "id": "test" }, - "test.table:md5,35d89a3811aa31711fc9815b6b80e6ec" + "test.recal.table:md5,35d89a3811aa31711fc9815b6b80e6ec" ] ], "1": [ @@ -117,7 +117,7 @@ { "id": "test" }, - "test.table:md5,35d89a3811aa31711fc9815b6b80e6ec" + "test.recal.table:md5,35d89a3811aa31711fc9815b6b80e6ec" ] ], "versions": [ @@ -127,9 +127,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "24.01.0" }, - "timestamp": "2024-02-13T16:16:42.135898" + "timestamp": "2024-02-26T07:59:25.266531501" }, "sarscov2 - bam": { "content": [ @@ -139,7 +139,7 @@ { "id": "test" }, - "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + "test.recal.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" ] ], "1": [ @@ -150,7 +150,7 @@ { "id": "test" }, - "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + "test.recal.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" ] ], "versions": [ @@ -160,8 +160,8 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "24.01.0" }, - "timestamp": "2024-02-13T16:14:57.629443" + "timestamp": "2024-02-26T07:58:31.908467001" } } \ No newline at end of file