nf-test tcoffee/seqreformat (nf-core#4435)

* Add nf-test for tcoffee/seqreformat * Remove pytest
louperelo · Nov 28, 2023 · b04c647 · b04c647
1 parent 1f253ec
commit b04c647
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Showing 11 changed files with 63 additions and 104 deletions.
diff --git a/modules/nf-core/tcoffee/seqreformat/main.nf.test b/modules/nf-core/tcoffee/seqreformat/main.nf.test
diff --git a/modules/nf-core/tcoffee/seqreformat/main.nf.test.snap b/modules/nf-core/tcoffee/seqreformat/main.nf.test.snap
diff --git a/modules/nf-core/tcoffee/seqreformat/meta.yml b/modules/nf-core/tcoffee/seqreformat/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html"
       tool_dev_url: "https://github.com/cbcrg/tcoffee"
       doi: "10.1006/jmbi.2000.4042"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
@@ -43,3 +43,4 @@ output:
 
 authors:
   - "@luisas"
+  - "@JoseEspinosa"
diff --git a/modules/nf-core/tcoffee/seqreformat/nextflow.config b/modules/nf-core/tcoffee/seqreformat/nextflow.config
diff --git a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test
@@ -0,0 +1,33 @@
+nextflow_process {
+
+    name "Test Process TCOFFEE_SEQREFORMAT"
+    script "../main.nf"
+    process "TCOFFEE_SEQREFORMAT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tcoffee"
+    tag "tcoffee/seqreformat"
+
+    test("sarscov2 - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ],
+                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                           ]
+                """
+            }
+        }
+
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.formatted_file).match("formatted_file")},
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap
diff --git a/modules/nf-core/tcoffee/seqreformat/tests/nextflow.config b/modules/nf-core/tcoffee/seqreformat/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = "-output=sim_idscore"
+}
diff --git a/modules/nf-core/tcoffee/seqreformat/tests/tags.yml b/modules/nf-core/tcoffee/seqreformat/tests/tags.yml
@@ -0,0 +1,2 @@
+tcoffee/seqreformat:
+  - "modules/nf-core/tcoffee/seqreformat/**"
diff --git a/tests/modules/nf-core/tcoffee/seqreformat/main.nf b/tests/modules/nf-core/tcoffee/seqreformat/main.nf
diff --git a/tests/modules/nf-core/tcoffee/seqreformat/nextflow.config b/tests/modules/nf-core/tcoffee/seqreformat/nextflow.config
diff --git a/tests/modules/nf-core/tcoffee/seqreformat/test.yml b/tests/modules/nf-core/tcoffee/seqreformat/test.yml