update paths for VEP (nf-core#5281)

update paths
tucano · Mar 20, 2024 · b69a8e7 · b69a8e7
1 parent dce2a09
commit b69a8e7
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
@@ -31,7 +31,7 @@ nextflow_process {
                 """
                 input[0] = Channel.of([
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true),
                     []
                 ])
                 input[1] = params.vep_genome
@@ -40,7 +40,7 @@ nextflow_process {
                 input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }
                 input[5] = Channel.value([
                     [id:"fasta"],
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ])
                 input[6] = []
                 """
@@ -76,7 +76,7 @@ nextflow_process {
                 """
                 input[0] = Channel.of([
                     [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true),
                     []
                 ])
                 input[1] = params.vep_genome
@@ -85,7 +85,7 @@ nextflow_process {
                 input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }
                 input[5] = Channel.value([
                     [id:"fasta"],
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ])
                 input[6] = []
                 """