Ported arcashla/extract to nf-test (#6225)

modules/nf-core/arcashla/extract/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/RabadanLab/arcasHLA"
       tool_dev_url: "https://github.com/RabadanLab/arcasHLA"
       doi: "10.1093/bioinformatics/btz474"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

modules/nf-core/arcashla/extract/tests/main.nf.test

@@ -0,0 +1,72 @@
+
+nextflow_process {
+
+    name "Test Process ARCASHLA_EXTRACT"
+    script "../main.nf"
+    process "ARCASHLA_EXTRACT"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "arcashla"
+    tag "arcashla/extract"
+
+    test("test-arcashla-extract") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+				]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.log[0]).text.contains('Converting bam to fastq') },
+                { assert snapshot(
+                    process.out.extracted_reads_fastq[0][1].collect { file(it).name },
+                    process.out.intermediate_bam[0][1].collect { bam(it).getReadsMD5() },
+                    file(process.out.intermediate_sam[0][1]).name,
+                    bam(process.out.intermediate_sorted_bam[0][1]).getReadsMD5(),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-arcashla-extract-single-end") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_single_end', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam', checkIfExists: true)
+				]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.log[0]).text.contains('Converting bam to fastq') },
+                { assert snapshot(
+                    file(process.out.extracted_reads_fastq[0][1]).name,
+                    process.out.intermediate_bam[0][1].collect { bam(it).getReadsMD5() },
+                    file(process.out.intermediate_sam[0][1]).name,
+                    bam(process.out.intermediate_sorted_bam[0][1]).getReadsMD5(),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+}

modules/nf-core/arcashla/extract/tests/main.nf.test.snap

@@ -0,0 +1,43 @@
+{
+    "test-arcashla-extract-single-end": {
+        "content": [
+            "test3.single_end.markduplicates.sorted.extracted.fq.gz",
+            [
+                "c7f49f93d2aebb68f128b85c6b6a36c0",
+                "13f0c075d7bfddcf19a48669bb69ae4c"
+            ],
+            "test3.single_end.markduplicates.sorted.hla.sam",
+            "13f0c075d7bfddcf19a48669bb69ae4c",
+            [
+                "versions.yml:md5,bad529c7a165615b9641e7780cc13160"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-21T12:36:32.699685"
+    },
+    "test-arcashla-extract": {
+        "content": [
+            [
+                "test.paired_end.sorted.extracted.1.fq.gz",
+                "test.paired_end.sorted.extracted.2.fq.gz"
+            ],
+            [
+                "ef014d5b0cd0903595da255cdce79662",
+                "ef014d5b0cd0903595da255cdce79662"
+            ],
+            "test.paired_end.sorted.hla.sam",
+            "ef014d5b0cd0903595da255cdce79662",
+            [
+                "versions.yml:md5,bad529c7a165615b9641e7780cc13160"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-21T12:30:28.486246"
+    }
+}

modules/nf-core/arcashla/extract/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: ARCASHLA_EXTRACT {
+        ext.args = '--unmapped --keep_files'
+    }
+}

tests/config/pytest_modules.yml

@@ -7,9 +7,6 @@ amps:
 angsd/contamination:
   - modules/nf-core/angsd/contamination/**
   - tests/modules/nf-core/angsd/contamination/**
-arcashla/extract:
-  - modules/nf-core/arcashla/extract/**
-  - tests/modules/nf-core/arcashla/extract/**
 arriba/arriba:
   - modules/nf-core/arriba/arriba/**
   - tests/modules/nf-core/arriba/arriba/**