Added nf-test for atlas/splitmerge (#6344)

Co-authored-by: Simon Pearce <[email protected]>

modules/nf-core/atlas/splitmerge/main.nf

@@ -11,7 +11,8 @@ process ATLAS_SPLITMERGE {
     tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist)
 
     output:
-    tuple val(meta), path("*_mergedReads.bam"), path("*.txt.gz"), emit: data
+    tuple val(meta), path("*_mergedReads.bam")  , emit: bam
+    tuple val(meta), path("*.txt.gz")           , emit: txt
     path "versions.yml", emit: versions
 
     when:

modules/nf-core/atlas/splitmerge/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
       tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
       doi: "10.1101/105346"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
@@ -27,7 +27,7 @@ input:
       type: file
       description: The BAI file for the input BAM file
       pattern: "*.bai"
-  - read_group_setting:
+  - read_group_settings:
       type: file
       description: |
         TXT file containing the split and merge settings for
@@ -55,7 +55,7 @@ output:
       type: file
       description: A BAM file with suffix_mergedReads.bam
       pattern: "*_mergedReads.bam"
-  - filelist:
+  - txt:
       type: file
       description: A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz
       pattern: "*.txt.gz"

modules/nf-core/atlas/splitmerge/tests/main.nf.test

@@ -0,0 +1,43 @@
+
+nextflow_process {
+
+    name "Test Process ATLAS_SPLITMERGE"
+    script "../main.nf"
+    process "ATLAS_SPLITMERGE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "atlas"
+    tag "atlas/splitmerge"
+
+    test("test-atlas-splitmerge") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/read_group_settings.txt', checkIfExists: true),
+                    []
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.txt[0][1]).linesGzip[3..7],
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/atlas/splitmerge/tests/main.nf.test.snap

@@ -0,0 +1,22 @@
+{
+    "test-atlas-splitmerge": {
+        "content": [
+            [
+                "Read testN:1, rev : not a proper pair (orphan)",
+                "Read testN:99, rev : longer than insert size (TLEN)",
+                "Read testN:99, rev : not a proper pair (orphan)",
+                "Read testN:830, rev : longer than insert size (TLEN)",
+                "Read testN:830, fwd : longer than insert size (TLEN)"
+            ],
+            "66f5f17da47cc4dced99bd17d739b536",
+            [
+                "versions.yml:md5,208f6ef7923cec00ddbcd5825f84a4fa"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T15:33:41.150912"
+    }
+}

tests/config/pytest_modules.yml

@@ -25,9 +25,6 @@ ataqv/ataqv:
 ataqv/mkarv:
   - modules/nf-core/ataqv/mkarv/**
   - tests/modules/nf-core/ataqv/mkarv/**
-atlas/splitmerge:
-  - modules/nf-core/atlas/splitmerge/**
-  - tests/modules/nf-core/atlas/splitmerge/**
 authentict/deam2cont:
   - modules/nf-core/authentict/deam2cont/**
   - tests/modules/nf-core/authentict/deam2cont/**