add mergeContext to methyldackel extract comprehensive + comprehensiv…

…e tests

CHANGELOG.md

@@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Pipeline Updates
 
--
+- 🔧 Add `--mergeContext` ext.arg to `methyldackel/extract` when running with `--comprehensive` param to merge metrics from individual Cytosines in a CpG, producing per-CpG metrics rather than per-Cytosine metrics [#460](https://github.com/nf-core/methylseq/pull/)
 
 ## [v3.0.0](https://github.com/nf-core/methylseq/releases/tag/3.0.0) - [2024-12-16]
 

conf/modules/methyldackel_extract.config

@@ -1,7 +1,7 @@
 process {
     withName: METHYLDACKEL_EXTRACT {
         ext.args = [
-            params.comprehensive ? ' --CHG --CHH' : '',
+            params.comprehensive ? ' --CHG --CHH --mergeContext' : '',
             params.ignore_flags ? " --ignoreFlags" : '',
             params.methyl_kit ? " --methylKit" : '',
             params.min_depth > 0 ? " --minDepth ${params.min_depth}" : ''

tests/bismark_comprehensive.nf.test

@@ -0,0 +1,41 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "../main.nf"
+    config "./nextflow.config"
+    tag "cpu"
+
+    test("Params: bismark | comprehensive") {
+        when {
+            params {
+                aligner       = "bismark"
+                comprehensive = true
+                outdir        = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"),
+                    // All stable path name
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All bam files
+                    bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
+}