Merge pull request #539 from atrigila/migrate_picard

Add nf-test to local module `ENSEMBL_DOWNLOAD`

Author: atrigila

.gitignore

@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 null/
+.nf-test*

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Normalized gene expression calculated [#488](https://github.com/nf-core/rnafusion/pull/488)
 - Primary assembly now used as main reference genome FASTA file, as recommended by the STAR manual [#488](https://github.com/nf-core/rnafusion/pull/488)
 - Use of only ensembl GTF file, not chr.gtf file as GTF reference file [#488](https://github.com/nf-core/rnafusion/pull/488)
+- Add nf-test to local module: `ENSEMBL_DOWNLOAD` [#508](https://github.com/nf-core/rnafusion/pull/508)
 
 ### Changed
 

modules/local/ensembl/tests/main.nf.test

@@ -0,0 +1,37 @@
+nextflow_process {
+
+    name "Test Process ENSEMBL_DOWNLOAD"
+    script "../main.nf"
+    process "ENSEMBL_DOWNLOAD"
+
+    test("Should download Ensembl files") {
+
+        when {
+            params {
+                outdir = "tests/results"
+                genome = "GRCh38"
+            }
+            process {
+                """
+                input[0] = "102"
+                input[1] = "GRCh38"
+                input[2] = "GRCh38"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.gtf[0][1]).name,
+                    file(process.out.primary_assembly[0][1]).name,
+                    file(process.out.chrgtf[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+}

modules/local/ensembl/tests/main.nf.test.snap

@@ -0,0 +1,17 @@
+{
+    "Should download Ensembl files": {
+        "content": [
+            "Homo_sapiens.GRCh38.102.gtf",
+            "Homo_sapiens.GRCh38.102.dna.primary_assembly.fa",
+            "Homo_sapiens.GRCh38.102.chr.gtf",
+            [
+                "versions.yml:md5,efb55665a151fe2b4d9eac70c0e01bb0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-26T14:06:24.319131837"
+    }
+}