Remove lib directory and replace it with granular utils_* subworkflows

nf_core/pipeline-template/conf/test.config

@@ -24,11 +24,8 @@ params {
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
-    {% if igenomes -%}
+    {% if igenomes %}
     // Genome references
     genome = 'R64-1-1'
-    {%- else -%}
-    // Fasta references
-    fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
     {%- endif %}
 }

nf_core/pipeline-template/main.nf

@@ -12,7 +12,19 @@
 */
 
 nextflow.enable.dsl = 2
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_pipeline_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_pipeline_pipeline'
 {% if igenomes %}
+include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_pipeline_pipeline'
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     GENOME PARAMETER VALUES
@@ -22,59 +34,72 @@ nextflow.enable.dsl = 2
 // TODO nf-core: Remove this line if you don't need a FASTA file
 //   This is an example of how to use getGenomeAttribute() to fetch parameters
 //   from igenomes.config using `--genome`
-params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
+params.fasta = getGenomeAttribute('fasta')
 {% endif %}
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    VALIDATE & PRINT PARAMETER SUMMARY
+    NAMED WORKFLOWS FOR PIPELINE
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { validateParameters; paramsHelp } from 'plugin/nf-validation'
+//
+// WORKFLOW: Run main analysis pipeline depending on type of input
+//
+workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
 
-// 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)
-}
+    take:
+    samplesheet // channel: samplesheet read in from --input
 
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
-}
+    main:
 
-WorkflowMain.initialise(workflow, params, log, args)
+    //
+    // WORKFLOW: Run pipeline
+    //
+    {{ short_name|upper }} ( 
+        samplesheet 
+    )
 
+}
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOW FOR PIPELINE
+    RUN MAIN WORKFLOW
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { {{ short_name|upper }} } from './workflows/{{ short_name }}'
+workflow {
 
-//
-// WORKFLOW: Run main {{ name }} analysis pipeline
-//
-workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
-    {{ short_name|upper }} ()
-}
+    main:
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN ALL WORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+    //
+    // SUBWORKFLOW: Run initialisation tasks
+    //
+    PIPELINE_INITIALISATION (
+        params.version,
+        params.help,
+        params.validate_params,
+        params.monochrome_logs,
+        params.outdir,
+        params.input
+    )
 
-//
-// WORKFLOW: Execute a single named workflow for the pipeline
-// See: https://github.com/nf-core/rnaseq/issues/619
-//
-workflow {
-    {{ prefix_nodash|upper }}_{{ short_name|upper }} ()
+    //
+    // WORKFLOW: Run main workflow
+    //
+    {{ prefix_nodash|upper }}_{{ short_name|upper }} (
+        PIPELINE_INITIALISATION.out.samplesheet
+    )
+
+    //
+    // SUBWORKFLOW: Run completion tasks
+    //
+    PIPELINE_COMPLETION (
+        params.email,
+        params.email_on_fail,
+        params.plaintext_email,
+        params.outdir,
+        params.monochrome_logs,
+        params.hook_url
+    )
 }
 
 /*