Enable tool selection for seqinspector

lib/SeqinspectorDataClasses.groovy

@@ -0,0 +1,25 @@
+// enum for the supported run modes
+
+public static enum RunMode {
+        FASTQ,
+        RUNFOLDER,
+    }
+
+// enum for the available tools
+
+public static enum Tool {
+        FASTQSCREEN,
+        FASTQC,
+        MULTIQC,
+    }
+
+// ToolProfile class to define and intersect selections of tools and handle extra arguments and settings
+
+public class ToolProfile {
+    Set<Tool> enable
+    Set<Tool> disable
+    Map<Tool, Map<String,String>> tool_arguments = [:]
+}
+
+
+

modules/local/utils_seqinspector_profiles/main.nf

@@ -0,0 +1,79 @@
+new GroovyShell().evaluate(new File("$projectDir/lib/SeqinspectorDataClasses.groovy"))
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+// Function to get a valid profile from a ToolProfiles map
+    /*
+    String profileStr,
+    Map<String, ToolProfile> toolProfilesMap
+    <logger> log
+    */
+
+def getProfileFromToolProfiles(profileStr, toolProfilesMap, log) {
+
+        if (!toolProfilesMap) {
+            toolProfilesMap = SeqinspectorDataClasses.ToolProfiles
+        }
+
+        if (!toolProfilesMap.containsKey(profileStr.toUpperCase())) {
+            def keys = toolProfilesMap.keySet().toLowerCase().join('\n  - ')
+            log.error "Invalid profile specified: '${profileStr}'. Valid options are:\n  - ${keys}"
+            nextflow.Nextflow.exit(1)
+        }
+        return toolProfilesMap[profileStr]
+    }
+
+
+// Function to combine two profiles
+    /*
+    String profileStr,
+    Map<String, ToolProfile> toolProfilesMap
+    <logger> log
+    */
+
+def combine_profiles(firstProfile, otherProfile, log) {
+
+     // Create a new ToolProfile instance to store the combined results
+    def combinedProfile = new SeqinspectorDataClasses.ToolProfile(
+        enable: (firstProfile.enable + otherProfile.enable),
+        disable: (firstProfile.disable + otherProfile.disable),
+        tool_arguments: [:]
+    )
+
+    // remove possibly disabled tools
+    combinedProfile.enable.removeAll(combinedProfile.disable)
+
+
+    // Combine tool_arguments maps
+    def allArgs = firstProfile.tool_arguments.keySet() + otherProfile.tool_arguments.keySet()
+    allArgs.each { tool ->
+        def firstArgs = firstProfile.tool_arguments[tool] ?: [:]
+        def otherArgs = otherProfile.tool_arguments[tool] ?: [:]
+
+        // Check for common arguments specified in both profiles for a tool
+        def commonArgs = firstArgs.keySet().intersect(otherArgs.keySet())
+        // if a common setting for a tool is detected, compare the values
+        if (commonArgs) {
+            def incompatibleArgs = false
+            commonArgs.each { arg ->
+                if(firstArgs[arg] != otherArgs[arg]) {
+                log.error "Conflicting settings of argument '${arg}' for tool '${tool}'"
+                incompatibleArgs = true
+                }
+            }
+            if(incompatibleArgs) {
+                nextflow.Nextflow.exit(1)
+            }
+        }
+        combinedProfile.tool_arguments[tool] = firstArgs + otherArgs
+    }
+
+    return combinedProfile
+
+
+}
+

modules/local/utils_seqinspector_tools/main.nf

@@ -0,0 +1,14 @@
+
+include { getEnumNames } from '../utils_seqinspector_validation/main.nf'
+
+new GroovyShell().evaluate(new File("$projectDir/lib/SeqinspectorDataClasses.groovy"))
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+def getAllToolNames() {
+        getEnumNames(SeqinspectorDataClasses.Tool)
+    }

modules/local/utils_seqinspector_validation/main.nf

@@ -0,0 +1,97 @@
+
+new GroovyShell().evaluate(new File("$projectDir/lib/SeqinspectorDataClasses.groovy"))
+
+/*
+========================================================================================
+    FUNCTIONS
+========================================================================================
+*/
+
+
+// Function to convert a string to an enum variant (enums give you a way of saying a value is one of a possible set of values)
+    /*
+    String s
+    Enum e
+    */
+
+
+def getEnumFromString(s, e) {
+    try {
+        return e.valueOf(s.toUpperCase())
+    } catch(java.lang.IllegalArgumentException err) {
+        return null
+    }
+}
+
+// Function to return all possible names of an enum
+    /*
+    Enum e
+    */
+
+def getEnumNames(e) {
+    e
+        .values()
+        *.name()
+        *.toLowerCase()
+}
+
+
+
+// Function to convert a comma-seperated string of tools to a list of Tool enums
+    /*
+    String tool_str
+    */
+
+def validateToolList(tool_str, log) {
+        if (!tool_str) {
+            return []
+        }
+        return tool_str
+            .tokenize(',')
+            .collect { token ->
+                try {
+                    return SeqinspectorDataClasses.Tool.valueOf(token.toUpperCase())
+                } catch(java.lang.IllegalArgumentException e) {
+                    def all_tools = getEnumNames(SeqinspectorDataClasses.Tool).join('\n  - ')
+                    log.error "Recieved invalid tool specification: '${token}'. Valid options are:\n  - ${all_tools}"
+                    nextflow.Nextflow.exit(1)
+                }
+            }
+            .unique()
+    }
+
+    // Function to check if the include and exclude lists have any common elements
+    /*
+    List<Enum> include_list
+    List<Enum> exclude_list
+    */
+
+def checkIncludeExcludeList(include_list, exclude_list, log) {
+        def common_tools = include_list + exclude_list
+            .countBy { it }
+            .findAll { k, v -> v > 1 }
+            .keySet()
+
+        if (common_tools) {
+            def common_tools_str = common_tools.values().join('\n  - ')
+            def message_base = 'The following tools were found in the include and the exclude lists!'
+            log.error "${message_base}:\n  - ${common_tools_str}"
+            nextflow.Nextflow.exit(1)
+        }
+}
+
+
+// Function to validate the run mode by comparing it to the enumerated values of a constant
+    /*
+    String run_mode
+    */
+
+def validateRunMode(run_mode, log) {
+    def run_mode_enum = getEnumFromString(run_mode, SeqinspectorDataClasses.RunMode)
+    if (!run_mode_enum) {
+        def run_modes_str = getEnumNames(SeqinspectorDataClasses.RunMode).join('\n  - ')
+        log.error "Invalid run mode selected: '${run_mode}'. Valid options are:\n  - ${run_modes_str}"
+        nextflow.Nextflow.exit(1)
+    }
+    return run_mode_enum
+}

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'

nextflow_schema.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/nextflow_schema.json",
     "title": "nf-core/seqinspector pipeline parameters",
     "description": "Pipeline to QC your sequences",
@@ -43,6 +43,40 @@
                 }
             }
         },
+        "tool_selection_options": {
+            "title": "Tool selection options",
+            "type": "object",
+            "description": "Select the quality checks and tools you wish to run.",
+            "default": "",
+            "properties": {
+                "tool_profile": {
+                    "type": "string",
+                    "default": "default",
+                    "description": "Pick and apply preconfigured profiles to select tools.",
+                    "fa_icon": "fab fa-blackberry",
+                    "pattern": "^\\w+(\\s(AND|OR|XOR|IAND)\\s\\w+)*$"
+                },
+                "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",
+                    "description": "Comma-seperated list of tools that you wish to run. The selection will be applied after the profiles and added to the final list.",
+                    "pattern": "^(\\w+(,\\s\\w+)*)?$"
+                },
+                "tools_exclude": {
+                    "type": "string",
+                    "fa_icon": "fas fa-search-minus",
+                    "description": "Comma-seperated list of tools that must not run. The selection will be subtracted from the evaluated profiles.",
+                    "pattern": "^(\\w+(,\\s\\w+)*)?$"
+                }
+            }
+        },
         "reference_genome_options": {
             "title": "Reference genome options",
             "type": "object",
@@ -280,6 +314,9 @@
         {
             "$ref": "#/definitions/input_output_options"
         },
+        {
+            "$ref": "#/definitions/tool_selection_options"
+        },
         {
             "$ref": "#/definitions/reference_genome_options"
         },

subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf

@@ -77,6 +77,38 @@ workflow PIPELINE_INITIALISATION {
     //
     validateInputParameters() // Runs additional validation that is not done by $projectDir/nextflow_schema.json
 
+    //
+    // Process the tool selection parameters to generate the final list of tools (processes) to run
+    //
+    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)
+        def tool_exclude_list = Utilities.getToolList(params.tools_exclude, log)
+
+        // Check for overlapping include and exclude list entries
+        Utilities.checkIncludeExcludeList(tool_include_list, tool_exclude_list, log)
+
+        // Convert the specified custom tools into a profile
+        def custom_tools = Utilities.buildToolTracker(tool_include_list, tool_exclude_list)
+
+        // Apply the custom tools to the existing tool profile: orOperation to activate the include_tools
+        seqinspector_tools =  seqinspector_tools.orOperation(custom_tools)
+
+        // Apply the custom tools to the existing tool profile: iAndOperation to deactivate the exclude_tools
+        seqinspector_tools =  seqinspector_tools.iAndOperation(custom_tools)
+    }
+
     //
     // Create channel from input file provided through params.input
     //

workflows/seqinspector.nf

@@ -32,6 +32,8 @@ workflow SEQINSPECTOR {
     ch_multiqc_extra_files = Channel.empty()
     ch_multiqc_reports     = Channel.empty()
 
+
+    if (seqinspector_tools['FASTQC']){
     //
     // MODULE: Run FastQC
     //
@@ -40,6 +42,7 @@ workflow SEQINSPECTOR {
     )
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    }
 
     //
     // Collate and save software versions