Added nf-test for pairtools/parse

nf-core · Aug 22, 2024 · 285cff6 · 285cff6
1 parent fe9614c
commit 285cff6
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Showing 7 changed files with 75 additions and 43 deletions.
diff --git a/modules/nf-core/pairtools/parse/tests/main.nf.test b/modules/nf-core/pairtools/parse/tests/main.nf.test
@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+    name "Test Process PAIRTOOLS_PARSE"
+    script "../main.nf"
+    process "PAIRTOOLS_PARSE"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pairtools"
+    tag "pairtools/parse"
+
+    test("test-pairtools-parse") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.sam', checkIfExists: true) ]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.chrom.sizes', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.pairsam[0][1]).linesGzip[3..7],
+					process.out.stat,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/pairtools/parse/tests/main.nf.test.snap b/modules/nf-core/pairtools/parse/tests/main.nf.test.snap
@@ -0,0 +1,30 @@
+{
+    "test-pairtools-parse": {
+        "content": [
+            [
+                "#chromsize: chr1 1000",
+                "#chromsize: chr2 1000",
+                "#samheader: @SQ\tSN:chr1\tLN:1000",
+                "#samheader: @SQ\tSN:chr2\tLN:1000",
+                "#samheader: @PG\tID:mock\tPN:mock\tVN:0.0.0\tCL:mock"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.raw.pairsam.stat:md5,054bf78ee4f0a4c447ad3eeb81f1f4ae"
+                ]
+            ],
+            [
+                "versions.yml:md5,2c8cb00722749f8e3831464a5057c519"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T11:17:35.185642"
+    }
+}
diff --git a/modules/nf-core/pairtools/parse/tests/nextflow.config b/modules/nf-core/pairtools/parse/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: PAIRTOOLS_PARSE {
+        ext.prefix = { "${meta.id}.raw" }
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1010,9 +1010,6 @@ pairtools/flip:
 pairtools/merge:
   - modules/nf-core/pairtools/merge/**
   - tests/modules/nf-core/pairtools/merge/**
-pairtools/parse:
-  - modules/nf-core/pairtools/parse/**
-  - tests/modules/nf-core/pairtools/parse/**
 pairtools/restrict:
   - modules/nf-core/pairtools/restrict/**
   - tests/modules/nf-core/pairtools/restrict/**

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