Added nf-test for bam2fastx/bam2fastq (#6343)

* Added nf-test for bam2fastx/bam2fastq * Swap to snapshot all --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · Aug 26, 2024 · 2a6fda4 · 2a6fda4
1 parent b8414dc
commit 2a6fda4
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Showing 6 changed files with 72 additions and 33 deletions.
diff --git a/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test
@@ -0,0 +1,37 @@
+
+nextflow_process {
+
+    name "Test Process BAM2FASTX_BAM2FASTQ"
+    script "../main.nf"
+    process "BAM2FASTX_BAM2FASTQ"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bam2fastx"
+    tag "bam2fastx/bam2fastq"
+
+    test("test-bam2fastx-bam2fastq") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam.pbi', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "test-bam2fastx-bam2fastq": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fastq.gz:md5,8abf16176fd1625998ee28590e1039b1"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1b954947255d9b2ad16d2c523258cceb"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fastq.gz:md5,8abf16176fd1625998ee28590e1039b1"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1b954947255d9b2ad16d2c523258cceb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T06:30:10.25178642"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -34,9 +34,6 @@ atlas/splitmerge:
 authentict/deam2cont:
   - modules/nf-core/authentict/deam2cont/**
   - tests/modules/nf-core/authentict/deam2cont/**
-bam2fastx/bam2fastq:
-  - modules/nf-core/bam2fastx/bam2fastq/**
-  - tests/modules/nf-core/bam2fastx/bam2fastq/**
 bamtools/convert:
   - modules/nf-core/bamtools/convert/**
   - tests/modules/nf-core/bamtools/convert/**

diff --git a/tests/modules/nf-core/bam2fastx/bam2fastq/main.nf b/tests/modules/nf-core/bam2fastx/bam2fastq/main.nf
diff --git a/tests/modules/nf-core/bam2fastx/bam2fastq/nextflow.config b/tests/modules/nf-core/bam2fastx/bam2fastq/nextflow.config
diff --git a/tests/modules/nf-core/bam2fastx/bam2fastq/test.yml b/tests/modules/nf-core/bam2fastx/bam2fastq/test.yml