move gatk4/mergevcfs to nf-test (nf-core#4913)

* move gatk4/mergevcfs to nf-test * Update modules/nf-core/gatk4/mergevcfs/tests/main.nf.test Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update modules/nf-core/gatk4/mergevcfs/tests/main.nf.test Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * fix tests * Delete modules/nf-core/gatk4/mergevcfs/tests/nextflow.config --------- Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
RSC-RP · Mar 20, 2024 · 79d2703 · 79d2703
1 parent 3fd1a27
commit 79d2703
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diff --git a/modules/nf-core/gatk4/mergevcfs/meta.yml b/modules/nf-core/gatk4/mergevcfs/meta.yml
@@ -29,7 +29,7 @@ input:
       description: |
         Groovy Map containing reference information
         e.g. [ id:'genome']
-  - ref_dict:
+  - dict:
       type: file
       description: Optional Sequence Dictionary as input
       pattern: "*.dict"

diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test
@@ -0,0 +1,87 @@
+nextflow_process {
+
+    name "Test Process GATK4_MERGEVCFS"
+    script "../main.nf"
+    process "GATK4_MERGEVCFS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/mergevcfs"
+
+    test("test_gatk4_mergevcfs") {
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true) ]]
+                input[1] = [ [], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        file(process.out.vcf.get(0).get(1)).name,
+                        file(process.out.tbi.get(0).get(1)).name
+                    ).match("test_gatk4_mergevcfs")
+                },
+            )
+        }
+
+    }
+
+    test("test_gatk4_mergevcfs_no_dict") {
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true) ]]
+                input[1] = [ [],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        file(process.out.vcf.get(0).get(1)).name,
+                        file(process.out.tbi.get(0).get(1)).name
+                    ).match("test_gatk4_mergevcfs_no_dict")
+                },
+            )
+        }
+
+    }
+
+    test("test_gatk4_mergevcfs_no_dict_stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true) ]]
+                input[1] = [ [],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        file(process.out.vcf.get(0).get(1)).name,
+                        file(process.out.tbi.get(0).get(1)).name
+                    ).match("test_gatk4_mergevcfs_no_dict_stub")
+                },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap
diff --git a/modules/nf-core/gatk4/mergevcfs/tests/tags.yml b/modules/nf-core/gatk4/mergevcfs/tests/tags.yml
@@ -0,0 +1,2 @@
+gatk4/mergevcfs:
+  - "modules/nf-core/gatk4/mergevcfs/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -822,9 +822,6 @@ gatk4/mergebamalignment:
 gatk4/mergemutectstats:
   - modules/nf-core/gatk4/mergemutectstats/**
   - tests/modules/nf-core/gatk4/mergemutectstats/**
-gatk4/mergevcfs:
-  - modules/nf-core/gatk4/mergevcfs/**
-  - tests/modules/nf-core/gatk4/mergevcfs/**
 gatk4/mutect2:
   - modules/nf-core/gatk4/mutect2/**
   - tests/modules/nf-core/gatk4/mutect2/**

diff --git a/tests/modules/nf-core/gatk4/mergevcfs/main.nf b/tests/modules/nf-core/gatk4/mergevcfs/main.nf
diff --git a/tests/modules/nf-core/gatk4/mergevcfs/nextflow.config b/tests/modules/nf-core/gatk4/mergevcfs/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/mergevcfs/test.yml b/tests/modules/nf-core/gatk4/mergevcfs/test.yml
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		gatk4/mergevcfs:
		- "modules/nf-core/gatk4/mergevcfs/**"