diff --git a/tests/software/bedtools/complement/main.nf b/tests/software/bedtools/complement/main.nf index a7e5c822..a20d73ec 100644 --- a/tests/software/bedtools/complement/main.nf +++ b/tests/software/bedtools/complement/main.nf @@ -6,9 +6,9 @@ include { BEDTOOLS_COMPLEMENT } from '../../../../software/bedtools/complement/m workflow test_bedtools_complement { input = [ [ id:'test'], - file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] - sizes = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.sizes", checkIfExists: true) + sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) BEDTOOLS_COMPLEMENT ( input, sizes ) } diff --git a/tests/software/bedtools/genomecov/main.nf b/tests/software/bedtools/genomecov/main.nf index c25c985c..01f02119 100644 --- a/tests/software/bedtools/genomecov/main.nf +++ b/tests/software/bedtools/genomecov/main.nf @@ -6,7 +6,7 @@ include { BEDTOOLS_GENOMECOV } from '../../../../software/bedtools/genomecov/mai workflow test_bedtools_genomecov { input = [ [ id:'test'], - file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.bam", checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ] BEDTOOLS_GENOMECOV ( input ) diff --git a/tests/software/bedtools/getfasta/main.nf b/tests/software/bedtools/getfasta/main.nf index 9fa64c38..641a4cba 100644 --- a/tests/software/bedtools/getfasta/main.nf +++ b/tests/software/bedtools/getfasta/main.nf @@ -5,8 +5,8 @@ nextflow.enable.dsl = 2 include { BEDTOOLS_GETFASTA } from '../../../../software/bedtools/getfasta/main.nf' addParams( options: [:] ) workflow test_bedtools_getfasta { - bed = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) ] - fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ] - + bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + BEDTOOLS_GETFASTA ( bed, fasta ) } diff --git a/tests/software/bedtools/intersect/main.nf b/tests/software/bedtools/intersect/main.nf index c9eaf4bf..dcfefdcb 100644 --- a/tests/software/bedtools/intersect/main.nf +++ b/tests/software/bedtools/intersect/main.nf @@ -6,8 +6,8 @@ include { BEDTOOLS_INTERSECT } from '../../../../software/bedtools/intersect/mai workflow test_bedtools_intersect { input = [ [ id:'test' ], - file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true), - file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test2.bed", checkIfExists: true) + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true) ] BEDTOOLS_INTERSECT ( input ) diff --git a/tests/software/bedtools/maskfasta/main.nf b/tests/software/bedtools/maskfasta/main.nf index 7deff269..eab7d71f 100644 --- a/tests/software/bedtools/maskfasta/main.nf +++ b/tests/software/bedtools/maskfasta/main.nf @@ -6,9 +6,9 @@ include { BEDTOOLS_MASKFASTA } from '../../../../software/bedtools/maskfasta/mai workflow test_bedtools_maskfasta { bed = [ [ id:'test'], - file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] - fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) ] - + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + BEDTOOLS_MASKFASTA ( bed, fasta ) } diff --git a/tests/software/bedtools/merge/main.nf b/tests/software/bedtools/merge/main.nf index 9c50a780..0407717e 100644 --- a/tests/software/bedtools/merge/main.nf +++ b/tests/software/bedtools/merge/main.nf @@ -6,7 +6,7 @@ include { BEDTOOLS_MERGE } from '../../../../software/bedtools/merge/main.nf' ad workflow test_bedtools_merge { input = [ [ id:'test'], - file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] BEDTOOLS_MERGE ( input ) diff --git a/tests/software/bedtools/slop/main.nf b/tests/software/bedtools/slop/main.nf index e4e697af..d9e4a7d3 100644 --- a/tests/software/bedtools/slop/main.nf +++ b/tests/software/bedtools/slop/main.nf @@ -6,10 +6,10 @@ include { BEDTOOLS_SLOP } from '../../../../software/bedtools/slop/main.nf' addP workflow test_bedtools_slop { input = [ [ id:'test'], - file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] - sizes = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.sizes", checkIfExists: true) - + sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + BEDTOOLS_SLOP ( input, sizes ) } diff --git a/tests/software/bedtools/sort/main.nf b/tests/software/bedtools/sort/main.nf index 6422ce7d..01f3f3c8 100644 --- a/tests/software/bedtools/sort/main.nf +++ b/tests/software/bedtools/sort/main.nf @@ -6,7 +6,7 @@ include { BEDTOOLS_SORT } from '../../../../software/bedtools/sort/main.nf' addP workflow test_bedtools_sort { input = [ [ id:'test'], - file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true) + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] BEDTOOLS_SORT ( input )