run_preseq param + skip preseq/lcextrap by default

CHANGELOG.md

@@ -12,7 +12,8 @@
 - 🔧 Install `fastq_align_dedup_bismark` subworkflow from nf-core/subworkflows [#453](https://github.com/nf-core/methylseq/pull/457)
 - 🔧 Install `fasta_index_bismark_bwameth` subworkflow from nf-core/subworkflows [#466](https://github.com/nf-core/methylseq/pull/)
 - 🔧 Install `fastq_align_dedup_bwameth` subworkflow from nf-core/subworkflows [#467](https://github.com/nf-core/methylseq/pull/)
-- 🔧 reorg individual configs to `conf/modules/` named configs [#459](https://github.com/nf-core/methylseq/pull/)
+- 🔧 reorg individual configs to `conf/modules/` named configs [#459](https://github.com/nf-core/methylseq/pull/469)
+- 🔧 `run_preseq` param + skip preseq/lcextrap module by default [#458](https://github.com/nf-core/methylseq/pull/470)
 
 ## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27]
 

conf/modules/preseq_lcextrap.config

@@ -5,12 +5,14 @@ process {
             [
                 path: { "${params.outdir}/${params.aligner}/preseq" },
                 mode: params.publish_dir_mode,
-                pattern: "*.txt"
+                pattern: "*.txt",
+                enabled: params.run_preseq
             ],
             [
                 path: { "${params.outdir}/${params.aligner}/preseq/log" },
                 mode: params.publish_dir_mode,
-                pattern: "*.log"
+                pattern: "*.log",
+                enabled: params.run_preseq
             ]
         ]
     }

nextflow.config

@@ -87,6 +87,9 @@ params {
     skip_deduplication         = false
     skip_multiqc               = false
 
+    // Run options
+    run_preseq                 = false
+
     // Boilerplate options
     outdir                       = null
     publish_dir_mode             = 'copy'

nextflow_schema.json

@@ -442,6 +442,20 @@
             },
             "fa_icon": "fas fa-fast-forward"
         },
+        "run_pipeline_steps": {
+            "title": "Run pipeline steps",
+            "type": "object",
+            "description": "",
+            "default": "",
+            "properties": {
+                "run_preseq": {
+                    "type": "boolean",
+                    "description": "Run preseq/lcextrap tool",
+                    "fa_icon": "fas fa-fast-forward"
+                }
+            },
+            "fa_icon": "fas fa-fast-forward"
+        },
         "institutional_config_options": {
             "title": "Institutional config options",
             "type": "object",
@@ -613,6 +627,9 @@
         {
             "$ref": "#/$defs/skip_pipeline_steps"
         },
+        {
+            "$ref": "#/$defs/run_pipeline_steps"
+        },
         {
             "$ref": "#/$defs/generic_options"
         },

tests/bismark_run_preseq.nf.test

@@ -0,0 +1,59 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "../main.nf"
+    config "./nextflow.config"
+
+    test("Params: bismark | run_preseq") {
+        when {
+            params {
+                outdir     = "$outputDir"
+                run_preseq = true
+            }
+        }
+
+        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_pipeline_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() }
+            )
+        }
+    }
+
+    test("Params: bismark | run_preseq with bowtie2-index") {
+        when {
+            params {
+                bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz"
+                outdir        = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    // Number of tasks
+                    workflow.trace.succeeded().size()
+                ).match() }
+            )
+        }
+    }
+
+}