Important! Template update for nf-core/tools v2.11

.github/workflows/ci.yml

@@ -28,7 +28,7 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.github/workflows/fix-linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php

.gitpod.yml

@@ -4,7 +4,9 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-
+  - name: unset JAVA_TOOL_OPTIONS
+    command: |
+      unset JAVA_TOOL_OPTIONS
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

assets/multiqc_config.yml

@@ -1,7 +1,9 @@
 report_comment: >
+
   This report has been generated by the <a href="https://github.com/nf-core/callingcards/releases/tag/1.0.0" target="_blank">nf-core/callingcards</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/callingcards/1.0.0/docs/output" target="_blank">documentation</a>.
+
 report_section_order:
   "nf-core-callingcards-methods-description":
     order: -1000

assets/slackreport.json

@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "nf-core/callingcards v${version} - ${runName}",
+            "author_name": "nf-core/callingcards ${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [

modules.json

@@ -293,4 +293,4 @@
             }
         }
     }
-}
+}

nextflow.config

@@ -102,6 +102,7 @@ profiles {
         dumpHashes             = true
         process.beforeScript   = 'echo $HOSTNAME'
         cleanup                = false
+        nextflow.enable.configProcessNamesValidation = true
     }
     conda {
         conda.enabled          = true
@@ -124,13 +125,13 @@ profiles {
     }
     docker {
         docker.enabled         = true
-        docker.userEmulation   = true
         conda.enabled          = false
         singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
+        runOptions             = '-u $(id -u):$(id -g)'
     }
     arm {
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
@@ -204,7 +205,7 @@ singularity.registry = 'quay.io'
 
 // Nextflow plugins
 plugins {
-    id '[email protected].1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id '[email protected].3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 // Load igenomes.config if required
@@ -227,6 +228,9 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
+// Disable process selector warnings by default. Use debug profile to enable warnings.
+nextflow.enable.configProcessNamesValidation = false
+
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
@@ -252,7 +256,7 @@ manifest {
     description     = """An automated processing pipeline for mammalian bulk calling cards experiments"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version = '1.0.0'
+    version         = '1.0.0'
     doi             = ''
 }