Added nf-test for pairtools/restrict (#6263)

nf-core · Aug 25, 2024 · 13b1571 · 13b1571
1 parent 3da38da
commit 13b1571
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Showing 7 changed files with 66 additions and 35 deletions.
diff --git a/modules/nf-core/pairtools/restrict/tests/main.nf.test b/modules/nf-core/pairtools/restrict/tests/main.nf.test
@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+    name "Test Process PAIRTOOLS_RESTRICT"
+    script "../main.nf"
+    process "PAIRTOOLS_RESTRICT"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pairtools"
+    tag "pairtools/restrict"
+
+    test("test-pairtools-restrict") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.4flip.pairs', checkIfExists: true)
+                ]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/frag.bed', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.restrict[0][1]).linesGzip[3..7],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/pairtools/restrict/tests/main.nf.test.snap b/modules/nf-core/pairtools/restrict/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "test-pairtools-restrict": {
+        "content": [
+            [
+                "#chromosomes: chr1 chr2",
+                "#chromsize: chr1 10000",
+                "#chromsize: chr2 10000",
+                "#samheader: @SQ\tSN:chr1\tLN:10000",
+                "#samheader: @SQ\tSN:chr2\tLN:10000"
+            ],
+            [
+                "versions.yml:md5,c67dacbd4b0c4f2f060bd65b776113da"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T11:15:44.880469"
+    }
+}
diff --git a/modules/nf-core/pairtools/restrict/tests/nextflow.config b/modules/nf-core/pairtools/restrict/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: PAIRTOOLS_RESTRICT {
+        ext.prefix = { "${meta.id}.restrict" }
+    }
+}
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/restrict:
-  - modules/nf-core/pairtools/restrict/**
-  - tests/modules/nf-core/pairtools/restrict/**
 panaroo/run:
   - modules/nf-core/panaroo/run/**
   - tests/modules/nf-core/panaroo/run/**

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