From 9391d7cf4d13dc32e73e10d60eff5f658be95f7b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 4 Nov 2025 13:46:54 +0100
Subject: [PATCH 1/2] simplify TEMPLATE with nf-core-utils 0.4.0

---
 nf_core/pipeline-template/nextflow.config     |  3 +-
 .../pipeline-template/workflows/pipeline.nf   | 36 ++++++-------------
 2 files changed, 12 insertions(+), 27 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index ccd9a797cb..b1ecae40ab 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -321,7 +321,8 @@ manifest {
 {% if nf_schema -%}
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.5.1'     // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-core-utils@0.4.0' // Helper functions for pipeline
 }
 
 validation {
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 94bdae9895..dc2f73af80 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -13,7 +13,7 @@ include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endi
 include { paramsSummaryMap       } from 'plugin/nf-schema'{% endif %}
 {%- if multiqc %}
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
-include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML } from 'plugin/nf-core-utils'
 {%- if citations or multiqc %}
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
 {%- endif %}
@@ -50,31 +50,15 @@ workflow {{ short_name|upper }} {
     //
     // Collate and save software versions
     //
-    def topic_versions = Channel.topic("versions")
-        .distinct()
-        .branch { entry ->
-            versions_file: entry instanceof Path
-            versions_tuple: true
-        }
-
-    def topic_versions_string = topic_versions.versions_tuple
-        .map { process, tool, version ->
-            [ process[process.lastIndexOf(':')+1..-1], "  ${tool}: ${version}" ]
-        }
-        .groupTuple(by:0)
-        .map { process, tool_versions ->
-            tool_versions.unique().sort()
-            "${process}:\n${tool_versions.join('\n')}"
-        }
-
-    softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
-        .mix(topic_versions_string)
-        .collectFile(
-            storeDir: "${params.outdir}/pipeline_info",
-            name: {% if is_nfcore %}'nf_core_'  + {% endif %} '{{ short_name }}_software_' {% if multiqc %} + 'mqc_' {% endif %} + 'versions.yml',
-            sort: true,
-            newLine: true
-        ).set { ch_collated_versions }
+    softwareVersionsToYAML(
+        softwareVersions: ch_versions.mix(channel.topic("versions")),
+        nextflowVersion: workflow.nextflow.version
+    ).collectFile(
+        storeDir: "${params.outdir}/pipeline_info",
+        name: {% if is_nfcore %}'nf_core_'  + {% endif %} '{{ short_name }}_software_' {% if multiqc %} + 'mqc_' {% endif %} + 'versions.yml',
+        sort: true,
+        newLine: true,
+    ).set { ch_collated_versions }
 
 {% if multiqc %}
     //

From 0771605cab644040b81f1cd223ca122bd9ec8d26 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 4 Nov 2025 12:48:04 +0000
Subject: [PATCH 2/2] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c9633bd0db..722b84afc6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@
 
 ### Template
 
+- simplify TEMPLATE with nf-core-utils 0.4.0 ([#3870](https://github.com/nf-core/tools/pull/3870))
+
 ### Linting
 
 ### Modules