Added nf-test for nextclade/datasetget (#6271)

* Added nf-test for nextclade/datasetget * Update modules/nf-core/nextclade/datasetget/tests/main.nf.test Co-authored-by: Joon Klaps <[email protected]> --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Joon Klaps <[email protected]>
nf-core · Aug 23, 2024 · e342fb1 · e342fb1
1 parent 30863c3
commit e342fb1
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Showing 7 changed files with 78 additions and 46 deletions.
diff --git a/modules/nf-core/nextclade/datasetget/meta.yml b/modules/nf-core/nextclade/datasetget/meta.yml
@@ -30,7 +30,7 @@ output:
       description: File containing software versions
       pattern: "versions.yml"
   - prefix:
-      type: path
+      type: directory
       description: A directory containing the dataset files needed for nextclade run
       pattern: "prefix"
 authors:

diff --git a/modules/nf-core/nextclade/datasetget/tests/main.nf.test b/modules/nf-core/nextclade/datasetget/tests/main.nf.test
@@ -0,0 +1,34 @@
+
+nextflow_process {
+
+    name "Test Process NEXTCLADE_DATASETGET"
+    script "../main.nf"
+    process "NEXTCLADE_DATASETGET"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "nextclade"
+    tag "nextclade/datasetget"
+
+    test("species-id-time") {
+
+        when {
+            process {
+                """
+                input[0] = 'sars-cov-2'
+				input[1] = 'MN908947'
+				input[2] = '2022-01-18T12:00:00Z'
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/nextclade/datasetget/tests/main.nf.test.snap b/modules/nf-core/nextclade/datasetget/tests/main.nf.test.snap
@@ -0,0 +1,43 @@
+{
+    "test-nextclade-datasetget": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "genemap.gff:md5,21ebebfd0f416eeb959e55ebffd808e8",
+                        "primers.csv:md5,5990c3483bf66ce607aeb90a44e7ef2e",
+                        "qc.json:md5,c512f51fda0212b21ffff05779180963",
+                        "reference.fasta:md5,c7ce05f28e4ec0322c96f24e064ef55c",
+                        "sequences.fasta:md5,41129d255b99e0e92bdf20e866b99a1b",
+                        "tag.json:md5,402ac2b87e2a6a64a3fbf5ad16497af3",
+                        "tree.json:md5,b8f32f547ff9e2131d6fc66b68fc54b1",
+                        "virus_properties.json:md5,5f2de3949e07cb633f3d9e4a7654dc81"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,12e8751f1d841b9aee87d31206c102a7"
+                ],
+                "dataset": [
+                    [
+                        "genemap.gff:md5,21ebebfd0f416eeb959e55ebffd808e8",
+                        "primers.csv:md5,5990c3483bf66ce607aeb90a44e7ef2e",
+                        "qc.json:md5,c512f51fda0212b21ffff05779180963",
+                        "reference.fasta:md5,c7ce05f28e4ec0322c96f24e064ef55c",
+                        "sequences.fasta:md5,41129d255b99e0e92bdf20e866b99a1b",
+                        "tag.json:md5,402ac2b87e2a6a64a3fbf5ad16497af3",
+                        "tree.json:md5,b8f32f547ff9e2131d6fc66b68fc54b1",
+                        "virus_properties.json:md5,5f2de3949e07cb633f3d9e4a7654dc81"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,12e8751f1d841b9aee87d31206c102a7"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T11:33:31.41372"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -974,9 +974,6 @@ ncbigenomedownload:
 ncbitools/vecscreen:
   - modules/nf-core/ncbitools/vecscreen/**
   - tests/modules/nf-core/ncbitools/vecscreen/**
-nextclade/datasetget:
-  - modules/nf-core/nextclade/datasetget/**
-  - tests/modules/nf-core/nextclade/datasetget/**
 nextclade/run:
   - modules/nf-core/nextclade/run/**
   - tests/modules/nf-core/nextclade/run/**

diff --git a/tests/modules/nf-core/nextclade/datasetget/main.nf b/tests/modules/nf-core/nextclade/datasetget/main.nf
diff --git a/tests/modules/nf-core/nextclade/datasetget/nextflow.config b/tests/modules/nf-core/nextclade/datasetget/nextflow.config
diff --git a/tests/modules/nf-core/nextclade/datasetget/test.yml b/tests/modules/nf-core/nextclade/datasetget/test.yml