Use INITIALISE subworkflow instead of WorkflowMain.initialise()

CHANGELOG.md

@@ -15,6 +15,7 @@
 - ([#2415](https://github.com/nf-core/tools/pull/2415#issuecomment-1709847086)) Add autoMounts for apptainer.
 - Remove `igenomes_base` from the schema, so that nf-validation doesn't create a file path and throw errors offline for s3 objects.
 - Update Gitpod profile resources to reflect base environment settings.
+- ([#2430](https://github.com/nf-core/tools/pull/2430)) - Use INITIALISE subworkflow to start pipeline and validate parameters etc.
 
 ### Download
 

nf_core/pipeline-template/lib/WorkflowMain.groovy

@@ -2,54 +2,8 @@
 // This file holds several functions specific to the main.nf workflow in the {{ name }} pipeline
 //
 
-import nextflow.Nextflow
-
 class WorkflowMain {
 
-    //
-    // Citation string for pipeline
-    //
-    public static String citation(workflow) {
-        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-            // TODO nf-core: Add Zenodo DOI for pipeline after first release
-            //"* The pipeline\n" +
-            //"  https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
-            "* The nf-core framework\n" +
-            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-            "* Software dependencies\n" +
-            "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-    }
-
-
-    //
-    // Validate parameters and print summary to screen
-    //
-    public static void initialise(workflow, params, log) {
-
-        // Print workflow version and exit on --version
-        if (params.version) {
-            String workflow_version = NfcoreTemplate.version(workflow)
-            log.info "${workflow.manifest.name} ${workflow_version}"
-            System.exit(0)
-        }
-
-        // Check that a -profile or Nextflow config has been provided to run the pipeline
-        NfcoreTemplate.checkConfigProvided(workflow, log)
-
-        // Check that conda channels are set-up correctly
-        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-            Utils.checkCondaChannels(log)
-        }
-
-        // Check AWS batch settings
-        NfcoreTemplate.awsBatch(workflow, params)
-
-        // Check input has been provided
-        if (!params.input) {
-            Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'")
-        }
-    }
-
     {%- if igenomes %}
     //
     // Get attribute from genome config file e.g. fasta

nf_core/pipeline-template/main.nf

@@ -30,23 +30,7 @@ params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { validateParameters; paramsHelp } from 'plugin/nf-validation'
-
-// Print help message if needed
-if (params.help) {
-    def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-    def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
-    log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
-    System.exit(0)
-}
-
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
-}
-
-WorkflowMain.initialise(workflow, params, log)
+include { INITIALISE } from './subworkflows/nf-core/initialise/main.nf'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -60,6 +44,8 @@ include { {{ short_name|upper }} } from './workflows/{{ short_name }}'
 // WORKFLOW: Run main {{ name }} analysis pipeline
 //
 workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
+    log.info NfcoreTemplate.logo(workflow, params.monochrome_logs)
+    INITIALISE(params.version, params.help, params.validate_params)
     {{ short_name|upper }} ()
 }
 

nf_core/pipeline-template/modules.json

@@ -21,6 +21,15 @@
                         "installed_by": ["modules"]
                     }
                 }
+            },
+            "subworkflows": {
+                "nf-core": {
+                    "initialise": {
+                        "branch": "master",
+                        "git_sha": "2a3d1b469385914c4eeca70f36bc378473049d93",
+                        "installed_by": ["subworkflows"]
+                    }
+                }
             }
         }
     }

nf_core/pipeline-template/workflows/pipeline.nf

@@ -4,16 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
-
-def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-def summary_params = paramsSummaryMap(workflow)
-
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
-
-Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.initialise(params, log)
+include { paramsSummaryMap } from 'plugin/nf-validation'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -59,6 +50,9 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
 // Info required for completion email and summary
 def multiqc_report = []
 
+// Get map of parameter values
+def summary_params = paramsSummaryMap(workflow)
+
 workflow {{ short_name|upper }} {
 
     ch_versions = Channel.empty()

tests/subworkflows/remove.py

@@ -12,6 +12,10 @@ def test_subworkflows_remove_uninstalled_subworkflow(self):
 
 def test_subworkflows_remove_subworkflow(self):
     """Test removing subworkflow and all it's dependencies after installing it"""
+    # Remove initialise subworkflow for clean slate
+    self.subworkflow_remove.remove("initialise")
+
+    # Install subworkflow
     self.subworkflow_install.install("bam_sort_stats_samtools")
 
     subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core")
@@ -34,6 +38,10 @@ def test_subworkflows_remove_subworkflow(self):
 
 def test_subworkflows_remove_subworkflow_keep_installed_module(self):
     """Test removing subworkflow and all it's dependencies after installing it, except for a separately installed module"""
+    # Remove initialise subworkflow for clean slate
+    self.subworkflow_remove.remove("initialise")
+
+    # Install subworkflow and module
     self.subworkflow_install.install("bam_sort_stats_samtools")
     self.mods_install.install("samtools/index")
 
@@ -44,6 +52,7 @@ def test_subworkflows_remove_subworkflow_keep_installed_module(self):
 
     mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json()
     assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
+
     mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json()
 
     assert Path.exists(subworkflow_path) is False

tests/subworkflows/update.py

@@ -162,6 +162,9 @@ def test_update_with_config_dont_update(self):
 
 def test_update_with_config_fix_all(self):
     """Fix the version of all nf-core subworkflows"""
+    # Remove intialise
+    self.subworkflow_remove.remove("initialise")
+
     # Install subworkflow at the latest version
     assert self.subworkflow_install.install("fastq_align_bowtie2")