INITIALISE uses take and emit (nf-core#3852)

* INTIALISE suboworkflow uses take and emit for better modularity

Changes:
 - INTIALISE subworkflow now uses a take to determine what to do
 - Use of take makes it work more portable (i.e. use your own params values!)
 - Emits the parameter summary map

* prettier

* INITIALISE meta.yml updated

* eclint

subworkflows/nf-core/initialise/main.nf

@@ -2,54 +2,67 @@
 // The role of this subworkflow is to check the input parameters and print help messages
 // Use this to start your nf-core pipeline
 
-include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation'
+include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation'
 
 workflow INITIALISE {
 
-    // Print workflow version and exit on --version
-    if (params.version) {
-        String version_string = ""
+    take:
+        version         // bool
+        help            // bool
+        validate_params // bool
 
-        if (workflow.manifest.version) {
-            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
-            version_string += "${prefix_v}${workflow.manifest.version}"
+    main:
+
+        // Print workflow version and exit on --version
+        if (version) {
+            String version_string = ""
+
+            if (workflow.manifest.version) {
+                def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+                version_string += "${prefix_v}${workflow.manifest.version}"
+            }
+
+            if (workflow.commitId) {
+                def git_shortsha = workflow.commitId.substring(0, 7)
+                version_string += "-g${git_shortsha}"
+            }
+            log.info "${workflow.manifest.name} ${version_string}"
+            System.exit(0)
+        }
+
+        // Print citation for nf-core
+        def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+            "* The nf-core framework\n" +
+            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+            "* Software dependencies\n" +
+            "  ${workflow.manifest.homePage}/blob/master/CITATIONS.md"
+        log.info citation
+
+        // Print help message if needed
+        if (params.help) {
+            def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv -profile docker"
+            log.info paramsHelp(command)
+            System.exit(0)
         }
 
-        if (workflow.commitId) {
-            def git_shortsha = workflow.commitId.substring(0, 7)
-            version_string += "-g${git_shortsha}"
+        if ( params.validate_params != false ){
+            validateParameters()
         }
-        log.info "${workflow.manifest.name} ${version_string}"
-        System.exit(0)
-    }
-
-    // Print citation for nf-core
-    def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  ${workflow.manifest.homePage}/blob/master/CITATIONS.md"
-    log.info citation
-
-    // Print help message if needed
-    if (params.help) {
-        def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv -profile docker"
-        log.info paramsHelp(command)
-        System.exit(0)
-    }
-
-    if ( params.validate_parameters != false ){
-        validateParameters()
-    }
-
-    if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-        log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-                "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-                "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-                "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-                "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-                "Please refer to the quick start section and usage docs for the pipeline.\n "
-    }
-
-    log.info paramsSummaryLog(workflow)
+
+        if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
+            log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
+                    "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
+                    "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
+                    "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
+                    "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
+                    "Please refer to the quick start section and usage docs for the pipeline.\n "
+        }
+
+        log.info paramsSummaryLog(workflow)
+
+        summary_params = paramsSummaryMap(workflow)
+
+    emit:
+        summary_params
+
 }

subworkflows/nf-core/initialise/meta.yml

@@ -8,6 +8,26 @@ keywords:
   - version
 modules:
 input:
+  - version:
+    type: boolean
+    description: |
+      Structure: val(version)
+      Boolean to show the pipeline version and exit.
+  - help:
+    type: boolean
+    description: |
+      Structure: val(help)
+      Boolean to show the pipeline help message and exit.
+  - validate_params:
+    type: boolean
+    description: |
+      Structure: val(validate_params)
+      Whether to validate the parameters prior to starting the pipeline.
 output:
+  - summary_params:
+    type: value
+    description: |
+      Structure: val(summary_params)
+      A map of the parameters used in the pipeline.
 authors:
   - "@adamrtalbot"

tests/subworkflows/nf-core/initialise/main.nf

@@ -5,5 +5,9 @@ nextflow.enable.dsl = 2
 include { INITIALISE } from '../../../../subworkflows/nf-core/initialise/main.nf'
 
 workflow test_initialise {
-    INITIALISE ( )
+    INITIALISE ( 
+        params.version,
+        params.help,
+        params.validate_params
+    )
 }

tests/subworkflows/nf-core/initialise/nextflow.config

@@ -1,7 +1,7 @@
 params {
     help                = false
     version             = false
-    validate_parameters = false
+    validate_params     = false
     test_data           = null
     monochrome_logs     = true
 }

tests/subworkflows/nf-core/initialise/nextflow_schema.json

@@ -12,7 +12,7 @@
             "description": "Define where the pipeline should find input data and save output data.",
             "required": ["outdir"],
             "properties": {
-                "validate_parameters": {
+                "validate_params": {
                     "type": "boolean",
                     "description": "Validate parameters?",
                     "default": true,