port htseq count pytest to nf-test (nf-core#5194)

* port htseq count pytest to nf-test * rename yml file * add extra line * fix tag.yml * fix meta.yml * fix meta.yml --------- Co-authored-by: zxBIB Grochowalski,Lukasz (GCBDS) EXTERNAL <[email protected]> Co-authored-by: Mauro Saporita <[email protected]>
jvfe · Mar 18, 2024 · 0a7b366 · 0a7b366
1 parent 298406d
commit 0a7b366
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Showing 5 changed files with 147 additions and 4 deletions.
diff --git a/modules/nf-core/htseq/count/meta.yml b/modules/nf-core/htseq/count/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://htseq.readthedocs.io/en/latest/"
       documentation: "https://htseq.readthedocs.io/en/latest/index.html"
       doi: "10.1093/bioinformatics/btu638"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

diff --git a/modules/nf-core/htseq/count/tests/main.nf.test b/modules/nf-core/htseq/count/tests/main.nf.test
@@ -0,0 +1,72 @@
+nextflow_process {
+
+    name "Test Process HTSEQ_COUNT"
+    script "../main.nf"
+    process "HTSEQ_COUNT"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "htseq"
+    tag "htseq/count"
+
+    test("bam input") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+
+                ]
+                input[1] = [
+                    [ id:'test2'], // meta map
+                    file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.txt.get(0).get(1) ==~ ".*.txt" },
+                { assert snapshot(process.out).match() }
+            )
+
+        }
+
+    }
+
+    test("cram input") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+
+                ]
+                input[1] = [
+                    [ id:'test2'], // meta map
+                    file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.txt.get(0).get(1) ==~ ".*.txt" },
+                { assert snapshot(process.out).match() }
+            )
+
+        }
+
+    }
+
+
+}
diff --git a/modules/nf-core/htseq/count/tests/main.nf.test.snap b/modules/nf-core/htseq/count/tests/main.nf.test.snap
diff --git a/modules/nf-core/htseq/count/tests/tags.yml b/modules/nf-core/htseq/count/tests/tags.yml
@@ -0,0 +1,2 @@
+htseq/count:
+  - "modules/nf-core/htseq/count/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1046,9 +1046,6 @@ homer/pos2bed:
 hpsuissero:
   - modules/nf-core/hpsuissero/**
   - tests/modules/nf-core/hpsuissero/**
-htseq/count:
-  - modules/nf-core/htseq/count/**
-  - tests/modules/nf-core/htseq/count/**
 hypo:
   - modules/nf-core/hypo/**
   - tests/modules/nf-core/hypo/**