Added nf-test for pairtools/dedup (#6267)

nf-core · Aug 23, 2024 · 1147cc4 · 1147cc4
1 parent b193226
commit 1147cc4
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Showing 7 changed files with 74 additions and 35 deletions.
diff --git a/modules/nf-core/pairtools/dedup/tests/main.nf.test b/modules/nf-core/pairtools/dedup/tests/main.nf.test
@@ -0,0 +1,39 @@
+
+nextflow_process {
+
+    name "Test Process PAIRTOOLS_DEDUP"
+    script "../main.nf"
+    process "PAIRTOOLS_DEDUP"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pairtools"
+    tag "pairtools/dedup"
+
+    test("test-pairtools-dedup") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.4dedup.pairsam', checkIfExists: true) ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.pairs[0][1]).linesGzip[3..7],
+					process.out.stat,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/pairtools/dedup/tests/main.nf.test.snap b/modules/nf-core/pairtools/dedup/tests/main.nf.test.snap
@@ -0,0 +1,30 @@
+{
+    "test-pairtools-dedup": {
+        "content": [
+            [
+                "#genome_assembly: unknown",
+                "#chromosomes: chr1 chr2",
+                "#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2",
+                "readid3\tchr1\t1\tchr1\t20\t+\t+\tUU\t.\t.",
+                "readid5\tchr1\t1\tchr1\t25\t+\t+\tUU\t.\t."
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.dedup.pairs.stat:md5,94682d1bc608ade150dd11993fbfd2a3"
+                ]
+            ],
+            [
+                "versions.yml:md5,485fbdd68f35d563c8559e1afedc4c53"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T11:23:16.451408"
+    }
+}
diff --git a/modules/nf-core/pairtools/dedup/tests/nextflow.config b/modules/nf-core/pairtools/dedup/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: PAIRTOOLS_DEDUP {
+        ext.prefix = { "${meta.id}.dedup" }
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -983,9 +983,6 @@ oncocnv:
 paftools/sam2paf:
   - modules/nf-core/paftools/sam2paf/**
   - test/modules/nf-core/paftools/sam2paf/**
-pairtools/dedup:
-  - modules/nf-core/pairtools/dedup/**
-  - tests/modules/nf-core/pairtools/dedup/**
 pairtools/parse:
   - modules/nf-core/pairtools/parse/**
   - tests/modules/nf-core/pairtools/parse/**

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