test(#119): Add a test for gzipped references

nf-core · Feb 14, 2024 · 2b32a6b · 2b32a6b
1 parent fbf44d4
commit 2b32a6b
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diff --git a/tests/pipeline/references.nf.test b/tests/pipeline/references.nf.test
@@ -26,6 +26,27 @@ nextflow_pipeline {
                 workflow.trace.tasks().size(),
             ).match()
         }
+    }
+
+    // https://github.com/nf-core/nascent/issues/119
+    test("Should work with gzipped references") {
+        // PINTS Fails because it doesn't find anything.
+        config 'tests/pipeline/skip_pints.config'
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "bwa"
+                fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genome.fasta.gz'
+                gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gtf.gz'
+            }
+        }
+
+        then {
+            assert workflow.failed
+            assert snapshot(
+                workflow.trace.tasks().size(),
+            ).match()
+        }
 
     }
 

diff --git a/tests/pipeline/references.nf.test.snap b/tests/pipeline/references.nf.test.snap
@@ -1,8 +1,22 @@
 {
+    "Should work with gzipped references": {
+        "content": [
+            0
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-14T15:02:05.680983538"
+    },
     "Should work with BWA Index": {
         "content": [
             127
         ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
         "timestamp": "2023-08-25T01:57:15+0000"
     }
 }