Added nf-test for picard/sortvcf (#6289)

nf-core · Aug 26, 2024 · eb3eb64 · eb3eb64
1 parent 3b584a9
commit eb3eb64
Show file tree

Hide file tree

Showing 6 changed files with 65 additions and 37 deletions.
diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test b/modules/nf-core/picard/sortvcf/tests/main.nf.test
@@ -0,0 +1,44 @@
+
+nextflow_process {
+
+    name "Test Process PICARD_SORTVCF"
+    script "../main.nf"
+    process "PICARD_SORTVCF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/sortvcf"
+
+    test("test-picard-sortvcf") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+				]
+				input[1] = [ [ id:'genome' ],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+				input[2] = [ [ id:'genome' ],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.vcf[0][1]).linesGzip[3..7],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "test-picard-sortvcf": {
+        "content": [
+            [
+                "##FILTER=<ID=PASS,Description=\"All filters passed\">",
+                "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
+                "##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">",
+                "##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes for each ALT allele, in the same order as listed\">",
+                "##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">"
+            ],
+            [
+                "versions.yml:md5,11949a1af95080dcc5bd1c75d68dee71"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T09:20:13.124551"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -962,9 +962,6 @@ picard/scatterintervalsbyns:
 picard/sortsam:
   - modules/nf-core/picard/sortsam/**
   - tests/modules/nf-core/picard/sortsam/**
-picard/sortvcf:
-  - modules/nf-core/picard/sortvcf/**
-  - tests/modules/nf-core/picard/sortvcf/**
 pindel/pindel:
   - modules/nf-core/pindel/pindel/**
   - tests/modules/nf-core/pindel/pindel/**

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