Update format

.github/workflows/ci.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "24.04.2"
+          - "25.10.4"
           - "latest-everything"
         profile:
           - "conda"

.github/workflows/nf-test.yml

@@ -65,8 +65,7 @@ jobs:
           - isMain: false
             tag: "samplesheet_target_regions_null"
         NXF_VER:
-          - "24.04.2"
-          - "24.10.5"
+          - "25.10.4"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

conf/test.config

@@ -25,7 +25,7 @@ params {
     input_type                  = 'ubam'      // Skip alignment step if input BAM/CRAM files are already aligned
     sequencing_platform         = 'ont'   // Sequencing platform (e.g. 'ont', 'hifi', 'pacbio'). You can also define the parameters through the minimap2_model or winnowmap_model
     minimap2_model              = null
-    use_winnowmap               = true  // Use Winnowmap for alignment instead of Minimap2
+    use_winnowmap               = false  // Use Winnowmap for alignment instead of Minimap2
     winnowmap_model             = null
     haplotag_bam                = true
     trio_analysis               = false  // Enable trio analysis for SNV calling and phasing

fix_editorconfig.py

@@ -107,6 +107,7 @@ def fix_nextflow_formatting(filepath):
     'subworkflows/local/call_str/main.nf',
     'subworkflows/local/haplotag_bam/main.nf',
     'subworkflows/local/longphase_variants/main.nf',
+    'subworkflows/local/utils_nfcore_longraredisease_pipeline/main.nf',
     'subworkflows/local/merge_sv/main.nf',
     'workflows/longraredisease.nf',
     'conf/test.config',

main.nf

@@ -1,75 +1,65 @@
-
-
-include {
-    longraredisease
-} from './workflows/longraredisease.nf'
-include {
-    PIPELINE_INITIALISATION
-} from './subworkflows/local/utils_nfcore_longraredisease_pipeline'
-include {
-    PIPELINE_COMPLETION
-} from './subworkflows/local/utils_nfcore_longraredisease_pipeline'
-include {
-    getGenomeAttribute
-} from './subworkflows/local/utils_nfcore_longraredisease_pipeline'
+#!/usr/bin/env nextflow
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Longrardisease
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Github : https://github.com/nf-core/longraredisease
+----------------------------------------------------------------------------------------
+*/
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    GENOME PARAMETER VALUES
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// 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`
+include { LONGRAREDISEASE  } from './workflows/longraredisease'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_longraredisease_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_longraredisease_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOWS FOR PIPELINE
+    RUN MAIN WORKFLOW
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-//
-// WORKFLOW: Run main analysis pipeline depending on type of input
-//
 workflow {
+
     main:
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
     PIPELINE_INITIALISATION (
-    params.version,
-    params.validate_params,
-    params.monochrome_logs,
-    args,
-    params.outdir,
-    params.input
+        params.version,
+        params.validate_params,
+        params.monochrome_logs,
+        args,
+        params.outdir,
+        params.input,
+        params.help,
+        params.help_full,
+        params.show_hidden
     )
+
     //
     // WORKFLOW: Run main workflow
     //
-    longraredisease(
+    LONGRAREDISEASE ()
 
-    )
     //
     // SUBWORKFLOW: Run completion tasks
     //
-    PIPELINE_COMPLETION(
-    params.email,
-    params.email_on_fail,
-    params.plaintext_email,
-    params.outdir,
-    params.monochrome_logs,
-    params.hook_url
+    PIPELINE_COMPLETION (
+        params.email,
+        params.email_on_fail,
+        params.plaintext_email,
+        params.outdir,
+        params.monochrome_logs,
+        params.hook_url,
+        Channel.empty() // FIXED: Added missing multiqc_report parameter
     )
 }
 
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN MAIN WORKFLOW
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END