add nf-test to gatk4/bedtointervallist - nf-core#3936 (nf-core#5251)

Co-authored-by: LE BARS Victor <Victor@ar155065.univ-rennes1.fr>
vlebars · Mar 20, 2024 · 8bdb60d · 8bdb60d
1 parent 322fa94
commit 8bdb60d
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Showing 7 changed files with 75 additions and 33 deletions.
diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test
@@ -0,0 +1,38 @@
+nextflow_process {
+
+    name "Test Process GATK4_BEDTOINTERVALLIST"
+    script "../main.nf"
+    process "GATK4_BEDTOINTERVALLIST"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/bedtointervallist"
+
+    test("test_gatk4_bedtointervallist") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                [file(params.modules_testdata_base_path + 
+                'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ]
+                ]
+                input[1] = [ [ id:'dict' ], // meta map
+                [file(params.modules_testdata_base_path +
+                'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap
diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/tags.yml b/modules/nf-core/gatk4/bedtointervallist/tests/tags.yml
@@ -0,0 +1,2 @@
+gatk4/bedtointervallist:
+  - "modules/nf-core/gatk4/bedtointervallist/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -707,9 +707,6 @@ gatk4/applyvqsr:
 gatk4/asereadcounter:
   - modules/nf-core/gatk4/asereadcounter/**
   - tests/modules/nf-core/gatk4/asereadcounter/**
-gatk4/bedtointervallist:
-  - modules/nf-core/gatk4/bedtointervallist/**
-  - tests/modules/nf-core/gatk4/bedtointervallist/**
 gatk4/calculatecontamination:
   - modules/nf-core/gatk4/calculatecontamination/**
   - tests/modules/nf-core/gatk4/calculatecontamination/**

diff --git a/tests/modules/nf-core/gatk4/bedtointervallist/main.nf b/tests/modules/nf-core/gatk4/bedtointervallist/main.nf
diff --git a/tests/modules/nf-core/gatk4/bedtointervallist/nextflow.config b/tests/modules/nf-core/gatk4/bedtointervallist/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/bedtointervallist/test.yml b/tests/modules/nf-core/gatk4/bedtointervallist/test.yml