Added nf-test for bedtools/slop

nf-core · Aug 26, 2024 · f3b3919 · f3b3919
1 parent 13b1571
commit f3b3919
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Showing 6 changed files with 71 additions and 30 deletions.
diff --git a/modules/nf-core/bedtools/slop/tests/main.nf.test b/modules/nf-core/bedtools/slop/tests/main.nf.test
@@ -0,0 +1,36 @@
+
+nextflow_process {
+
+    name "Test Process BEDTOOLS_SLOP"
+    script "../main.nf"
+    process "BEDTOOLS_SLOP"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bedtools"
+    tag "bedtools/slop"
+
+    test("test-bedtools-slop") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/bedtools/slop/tests/main.nf.test.snap b/modules/nf-core/bedtools/slop/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "test-bedtools-slop": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_out.bed:md5,4f1d8924925fe5d205c9e1981fe290a4"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ee6210f0a2c4a60d9cad324bfe18e0cf"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_out.bed:md5,4f1d8924925fe5d205c9e1981fe290a4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ee6210f0a2c4a60d9cad324bfe18e0cf"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T13:52:04.945029"
+    }
+}
diff --git a/...les/nf-core/bedtools/slop/nextflow.config → ...-core/bedtools/slop/tests/nextflow.config b/...les/nf-core/bedtools/slop/nextflow.config → ...-core/bedtools/slop/tests/nextflow.config
@@ -1,10 +1,6 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: BEDTOOLS_SLOP {
         ext.args = '-l 15 -r 30'
         ext.prefix = { "${meta.id}_out" }
     }
-
 }
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -115,9 +115,6 @@ bedtools/multiinter:
 bedtools/shift:
   - modules/nf-core/bedtools/shift/**
   - tests/modules/nf-core/bedtools/shift/**
-bedtools/slop:
-  - modules/nf-core/bedtools/slop/**
-  - tests/modules/nf-core/bedtools/slop/**
 bedtools/split:
   - modules/nf-core/bedtools/split/**
   - tests/modules/nf-core/bedtools/split/**

diff --git a/tests/modules/nf-core/bedtools/slop/main.nf b/tests/modules/nf-core/bedtools/slop/main.nf
diff --git a/tests/modules/nf-core/bedtools/slop/test.yml b/tests/modules/nf-core/bedtools/slop/test.yml