correctly run tests

nf-core · Mar 5, 2025 · 69f190f · 69f190f
1 parent e04af45
commit 69f190f
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Showing 3 changed files with 15 additions and 14 deletions.
diff --git a/subworkflows/local/prepare_alignment/tests/main.nf.test.snap b/subworkflows/local/prepare_alignment/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram",
+                        "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram",
                         "test.rna.paired_end.sorted.cram.crai"
                     ]
                 ],
@@ -20,7 +20,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-03-05T13:36:56.176207564"
+        "timestamp": "2025-03-05T14:42:59.447861122"
     },
     "bam, cram - no index, index": {
         "content": [
@@ -30,14 +30,14 @@
                         {
                             "id": "test"
                         },
-                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam",
+                        "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam",
                         "test.rna.paired_end.sorted.bam.bai"
                     ],
                     [
                         {
                             "id": "test"
                         },
-                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram",
+                        "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram",
                         "test.rna.paired_end.sorted.cram.crai"
                     ]
                 ],
@@ -50,7 +50,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-03-05T13:37:07.592019675"
+        "timestamp": "2025-03-05T14:43:15.493280437"
     },
     "only bam": {
         "content": [
@@ -60,7 +60,7 @@
                         {
                             "id": "test"
                         },
-                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam",
+                        "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam",
                         "test.rna.paired_end.sorted.bam.bai"
                     ]
                 ],
@@ -73,6 +73,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-03-05T13:32:21.806173639"
+        "timestamp": "2025-03-05T14:42:44.032096236"
     }
 }
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
@@ -23,7 +23,7 @@
                         {
                             "id": "dict"
                         },
-                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.dict"
+                        "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/genome/genome.dict"
                     ]
                 ],
                 "exon_bed": [
@@ -39,7 +39,7 @@
                         {
                             "id": "fasta"
                         },
-                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta"
+                        "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/genome/genome.fasta"
                     ]
                 ],
                 "fasta_fai": [
@@ -55,7 +55,7 @@
                         {
                             "id": "gtf"
                         },
-                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf"
+                        "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/genome/genome.gtf"
                     ]
                 ],
                 "known_indels": [
@@ -106,7 +106,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-03-05T13:22:39.746029169"
+        "timestamp": "2025-03-05T14:45:47.366394095"
     },
     "only essentials": {
         "content": [
@@ -152,7 +152,7 @@
                         {
                             "id": "fasta"
                         },
-                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta"
+                        "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/genome/genome.fasta"
                     ]
                 ],
                 "fasta_fai": [
@@ -168,7 +168,7 @@
                         {
                             "id": "gtf"
                         },
-                        "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf"
+                        "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/genome/genome.gtf"
                     ]
                 ],
                 "known_indels": [
@@ -216,6 +216,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-03-05T13:18:52.117370876"
+        "timestamp": "2025-03-05T14:45:25.808187589"
     }
 }
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -9,6 +9,7 @@
 
 params {
     modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+    pipelines_testdata_base_path = 'https://github.com/nf-core/test-datasets/raw/refs/heads/rnavar/data'
 }
 
 process {