Added nf-test for gatk4/filterintervals

nf-core · Aug 26, 2024 · 245f8b7 · 245f8b7
1 parent 13b1571
commit 245f8b7
Show file tree

Hide file tree

Showing 6 changed files with 73 additions and 40 deletions.
diff --git a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test
@@ -0,0 +1,38 @@
+
+nextflow_process {
+
+    name "Test Process GATK4_FILTERINTERVALS"
+    script "../main.nf"
+    process "GATK4_FILTERINTERVALS"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/filterintervals"
+
+    test("test-gatk4-filterintervals") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.preprocessed_intervals.interval_list', checkIfExists: true)
+				]
+				input[1] = [ [:], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.preprocessed_intervals.counts.tsv', checkIfExists: true) ] ]
+				input[2] = [ [:], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.annotated_intervals.tsv', checkIfExists: true) ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "test-gatk4-filterintervals": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.interval_list:md5,67b15dff732693db3542e6b1dc30a5da"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,9a445090a815c06982d5deb5ed7d5e30"
+                ],
+                "interval_list": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.interval_list:md5,67b15dff732693db3542e6b1dc30a5da"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9a445090a815c06982d5deb5ed7d5e30"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:25:35.933532"
+    }
+}
diff --git a/...ore/gatk4/filterintervals/nextflow.config → ...tk4/filterintervals/tests/nextflow.config b/...ore/gatk4/filterintervals/nextflow.config → ...tk4/filterintervals/tests/nextflow.config
@@ -1,9 +1,5 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: GATK4_FILTERINTERVALS {
         ext.args = "--interval-merging-rule OVERLAPPING_ONLY"
     }
-
 }
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -467,9 +467,6 @@ gatk4/determinegermlinecontigploidy:
 gatk4/fastqtosam:
   - modules/nf-core/gatk4/fastqtosam/**
   - tests/modules/nf-core/gatk4/fastqtosam/**
-gatk4/filterintervals:
-  - modules/nf-core/gatk4/filterintervals/**
-  - tests/modules/nf-core/gatk4/filterintervals/**
 gatk4/filtervarianttranches:
   - modules/nf-core/gatk4/filtervarianttranches/**
   - tests/modules/nf-core/gatk4/filtervarianttranches/**

diff --git a/tests/modules/nf-core/gatk4/filterintervals/main.nf b/tests/modules/nf-core/gatk4/filterintervals/main.nf
diff --git a/tests/modules/nf-core/gatk4/filterintervals/test.yml b/tests/modules/nf-core/gatk4/filterintervals/test.yml