Added nf-test for pairix (#6268)

nf-core · Aug 23, 2024 · c43d74f · c43d74f
1 parent aa51242
commit c43d74f
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Showing 7 changed files with 73 additions and 30 deletions.
diff --git a/modules/nf-core/pairix/meta.yml b/modules/nf-core/pairix/meta.yml
@@ -4,6 +4,8 @@ description: |
   containing pairs of genomic coordinates
 keywords:
   - index
+  - block-compressed
+  - pairs
 tools:
   - pairix:
       description: 2D indexing on bgzipped text files of paired genomic coordinates

diff --git a/modules/nf-core/pairix/tests/main.nf.test b/modules/nf-core/pairix/tests/main.nf.test
@@ -0,0 +1,32 @@
+
+nextflow_process {
+
+    name "Test Process PAIRIX"
+    script "../main.nf"
+    process "PAIRIX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pairix"
+
+    test("test-pairix") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				file("https://raw.githubusercontent.com/4dn-dcic/pairix/master/samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz", checkIfExists: true) ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/pairix/tests/main.nf.test.snap b/modules/nf-core/pairix/tests/main.nf.test.snap
@@ -0,0 +1,39 @@
+{
+    "test-pairix": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "4dn.bsorted.chr21_22_only.nontriangle.pairs.gz:md5,ee90dc99987ece492d598ed939d54561",
+                        "4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2:md5,a6e41cc7cff16fd15b5ee505549ec99a"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,848c8be602ec36645d30010ea30f0684"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "4dn.bsorted.chr21_22_only.nontriangle.pairs.gz:md5,ee90dc99987ece492d598ed939d54561",
+                        "4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2:md5,a6e41cc7cff16fd15b5ee505549ec99a"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,848c8be602ec36645d30010ea30f0684"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T11:25:18.874503"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -998,9 +998,6 @@ oncocnv:
 paftools/sam2paf:
   - modules/nf-core/paftools/sam2paf/**
   - test/modules/nf-core/paftools/sam2paf/**
-pairix:
-  - modules/nf-core/pairix/**
-  - tests/modules/nf-core/pairix/**
 pairtools/dedup:
   - modules/nf-core/pairtools/dedup/**
   - tests/modules/nf-core/pairtools/dedup/**

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