Modify parameters and continue refactor.

nf-core · Oct 22, 2024 · 64cc996 · 64cc996
1 parent 0c3f7cd
commit 64cc996
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Showing 7 changed files with 32 additions and 9 deletions.
diff --git a/lib/SeqinspectorDataClasses.groovy b/lib/SeqinspectorDataClasses.groovy
@@ -1,21 +1,21 @@
 // enum for the supported run modes
 
-static enum RunMode {
+public static enum RunMode {
         FASTQ,
         RUNFOLDER,
     }
 
 // enum for the available tools
 
-static enum Tool {
+public static enum Tool {
         FASTQSCREEN,
         FASTQC,
         MULTIQC,
     }
 
 // ToolProfile class to define and intersect selections of tools and handle extra arguments and settings
 
-class ToolProfile {
+public class ToolProfile {
     Set<Tool> enable
     Set<Tool> disable
     Map<Tool, Map<String,String>> tool_arguments = [:]

diff --git a/modules/local/utils_seqinspector_profiles/main.nf b/modules/local/utils_seqinspector_profiles/main.nf
@@ -1,3 +1,5 @@
+new GroovyShell().evaluate(new File("$projectDir/lib/SeqinspectorDataClasses.groovy"))
+
 /*
 ========================================================================================
     FUNCTIONS

diff --git a/modules/local/utils_seqinspector_tools/main.nf b/modules/local/utils_seqinspector_tools/main.nf
@@ -1,6 +1,8 @@
 
 include { getEnumNames } from '../utils_seqinspector_validation/main.nf'
 
+new GroovyShell().evaluate(new File("$projectDir/lib/SeqinspectorDataClasses.groovy"))
+
 /*
 ========================================================================================
     FUNCTIONS

diff --git a/modules/local/utils_seqinspector_validation/main.nf b/modules/local/utils_seqinspector_validation/main.nf
@@ -1,3 +1,6 @@
+
+new GroovyShell().evaluate(new File("$projectDir/lib/SeqinspectorDataClasses.groovy"))
+
 /*
 ========================================================================================
     FUNCTIONS

diff --git a/nextflow.config b/nextflow.config
@@ -25,6 +25,12 @@ params {
     max_multiqc_email_size     = '25.MB'
     multiqc_methods_description = null
 
+    // Tool selection options
+    tool_profile               = 'default'
+    tool_profile_custom_path   = null
+    tools_include              = null
+    tools_exclude              = null
+
     // Boilerplate options
     outdir                       = null
     publish_dir_mode             = 'copy'

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -49,13 +49,20 @@
             "description": "Select the quality checks and tools you wish to run.",
             "default": "",
             "properties": {
-                "tool_selection": {
+                "tool_profile": {
                     "type": "string",
                     "default": "default",
-                    "description": "Pick and apply profiles to select tools. Choose from the profiles `none`, `minimal`,`default`, `all` and the operations `AND`, `OR`, `XOR` as well as `IAND`.",
+                    "description": "Pick and apply preconfigured profiles to select tools.",
                     "fa_icon": "fab fa-blackberry",
                     "pattern": "^\\w+(\\s(AND|OR|XOR|IAND)\\s\\w+)*$"
                 },
+                "tool_profile_custom_path": {
+                    "type": "string",
+                    "description": "Path to a custom profile used instead of the preconfigured ones.",
+                    "format": "file-path",
+                    "mimetype": "text/vnd.yaml",
+                    "fa_icon": "fas fa-clipboard-list"
+                },
                 "tools_include": {
                     "type": "string",
                     "fa_icon": "fas fa-search-plus",
@@ -68,8 +75,7 @@
                     "description": "Comma-seperated list of tools that must not run. The selection will be subtracted from the evaluated profiles.",
                     "pattern": "^(\\w+(,\\s\\w+)*)?$"
                 }
-            },
-            "required": ["tool_selection"]
+            }
         },
         "reference_genome_options": {
             "title": "Reference genome options",

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -80,13 +80,17 @@ workflow PIPELINE_INITIALISATION {
     //
     // Process the tool selection parameters to generate the final list of tools (processes) to run
     //
-    def seqinspector_tools = Constants.ToolProfiles["NONE"]  // Start with no tools (except MultiQC)
+    def seqinspector_tools = new SeqinspectorDataClasses.ToolProfile()  // Start with no tools (except MultiQC)
 
+
+    if(path.tool_profile_custom_path){
+
+    } else {
     // Activate the tools that are selected through the applied profiles (typically `default`)
     if (params.tool_selection) {
         def evaluated_profiles = Utilities.parseAndApplyBooleanOperation(params.tool_selection, Constants.ToolProfiles, log)
         seqinspector_tools = seqinspector_tools.orOperation(evaluated_profiles)
-    }
+    }}
 
     if (params.tools_include || params.tools_exclude) {
         def tool_include_list = Utilities.getToolList(params.tools_include, log)