Changed paths of files used in main.nf.test from test-data/methylseq … (

#7212) * cnanged paths of files used in main.nf.test from test-data/methylseq to test-data/modules * modified paths to include 'params.modules_testdata_base_path +' * removed extra ' in front of params --------- Co-authored-by: provatap <[email protected]> Co-authored-by: Sateesh_Peri <[email protected]>
nf-core · Dec 13, 2024 · e8e387e · e8e387e
1 parent 3a36acc
commit e8e387e
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
@@ -19,7 +19,7 @@ nextflow_process {
                 """
                 input[0] = Channel.of([
                     [ id:'test' ], // meta map
-                    file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
                 ])
                 """
             }
@@ -34,12 +34,12 @@ nextflow_process {
                 input[0] = Channel.of([
 				    [ id:'test', single_end:true ], // meta map
 				    [
-				        file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
+				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/illumina/SRR389222_sub1.fastq.gz', checkIfExists: true)
 				    ]
 				])
                 input[1] = Channel.of([
                     [ id:'test' ], // meta map
-                    file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
                 ])
 				input[2] = BWAMETH_INDEX.out.index
                 input[3] = []
@@ -68,12 +68,12 @@ nextflow_process {
                 input[0] = Channel.of([
 				    [ id:'test', single_end:true ], // meta map
 				    [
-				        file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
+				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/illumina/SRR389222_sub1.fastq.gz', checkIfExists: true)
 				    ]
 				])
                 input[1] = Channel.of([
                     [ id:'test' ], // meta map
-                    file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
                 ])
 				input[2] = BWAMETH_INDEX.out.index
                 input[3] = []
@@ -98,13 +98,13 @@ nextflow_process {
                 input[0] = Channel.of([
 				    [ id:'test', single_end:false ], // meta map
 				    [
-				        file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true),
-                        file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/illumina/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/illumina/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true),
 				    ]
 				])
                 input[1] = Channel.of([
                     [ id:'test' ], // meta map
-                    file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)
                 ])
 				input[2] = BWAMETH_INDEX.out.index
                 input[3] = []