diff --git a/tests/software/adapterremoval/main.nf b/tests/software/adapterremoval/main.nf index 90bcd638..87a7fadf 100644 --- a/tests/software/adapterremoval/main.nf +++ b/tests/software/adapterremoval/main.nf @@ -6,7 +6,7 @@ include { ADAPTERREMOVAL } from '../../../software/adapterremoval/main.nf' addPa workflow test_adapterremoval_single_end { input = [ [ id:'test', single_end:true, collapse:false ], // meta map - file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] ADAPTERREMOVAL ( input ) @@ -14,8 +14,8 @@ workflow test_adapterremoval_single_end { workflow test_adapterremoval_paired_end { input = [ [ id:'test', single_end:false, collapse:false ], // meta map - [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] ADAPTERREMOVAL ( input ) @@ -23,8 +23,8 @@ workflow test_adapterremoval_paired_end { workflow test_adapterremoval_paired_end_collapse { input = [ [ id:'test', single_end:false, collapse:true ], // meta map - [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] ADAPTERREMOVAL ( input ) diff --git a/tests/software/dsh/filterbed/main.nf b/tests/software/dsh/filterbed/main.nf index 404edce5..c3b9cadb 100644 --- a/tests/software/dsh/filterbed/main.nf +++ b/tests/software/dsh/filterbed/main.nf @@ -6,7 +6,7 @@ include { DSH_FILTERBED } from '../../../../software/dsh/filterbed/main.nf' addP workflow test_dsh_filterbed { input = [ [ id:'test' ], // meta map - [ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) ] + [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] ] DSH_FILTERBED ( input ) diff --git a/tests/software/dsh/splitbed/main.nf b/tests/software/dsh/splitbed/main.nf index a03d8cf2..11d0861e 100644 --- a/tests/software/dsh/splitbed/main.nf +++ b/tests/software/dsh/splitbed/main.nf @@ -6,7 +6,7 @@ include { DSH_SPLITBED } from '../../../../software/dsh/splitbed/main.nf' addPar workflow test_dsh_splitbed { input = [ [ id:'test' ], // meta map - [ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) ] + [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] ] DSH_SPLITBED ( input )