nf-core · mashehu · Oct 9, 2025 · Oct 7, 2025 · Oct 7, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -32,6 +32,7 @@
 ### Subworkflows
 
 - Linting of patched subworkflows ([#3755](https://github.com/nf-core/tools/pull/3755))
+- Update the utils_nfschema_plugin subworkflow to the latest version ([#3814](https://github.com/nf-core/tools/pull/3814))
 
 ### General
 

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
@@ -33,7 +33,7 @@
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
+                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
                         "installed_by": ["subworkflows"]
                     }{% endif %}
                 }

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -44,10 +44,21 @@ workflow PIPELINE_INITIALISATION {
     main:
 
     ch_versions = Channel.empty()
+
+    //
+    // Print version and exit if required and dump pipeline parameters to JSON file
+    //
+    UTILS_NEXTFLOW_PIPELINE (
+        version,
+        true,
+        outdir,
+        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
+    )
+
     {%- if nf_schema %}
 
     //
-    // Print help message
+    // Validate parameters and generate parameter summary to stdout
     //
 
     {%- if is_nfcore %}
@@ -68,44 +79,19 @@ workflow PIPELINE_INITIALISATION {
 * Software dependencies
     https://github.com/{{ name }}/blob/{{ default_branch }}/CITATIONS.md
 """{% endif %}
-    command = "nextflow run {${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-
-    if(help || help_full) {
-        log.info paramsHelp(
-            params.help instanceof String ? params.help : "",
-            {%- if is_nfcore %}
-            beforeText: before_text,
-            afterText: after_text,{% endif %}
-            command: command,
-            showHidden: show_hidden,
-            fullHelp: help_full
-        )
-        exit 0
-    }
-    {%- endif %}
+    command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
 
-    //
-    // Print version and exit if required and dump pipeline parameters to JSON file
-    //
-    UTILS_NEXTFLOW_PIPELINE (
-        version,
-        true,
-        outdir,
-        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
-    )
-
-    {%- if nf_schema %}
-
-    //
-    // Validate parameters and generate parameter summary to stdout
-    //
-    {% if is_nfcore -%}log.info(before_text){%- endif %}
     UTILS_NFSCHEMA_PLUGIN (
         workflow,
         validate_params,
-        null
+        null,
+        help,
+        help_full,
+        show_hidden,
+        {% if is_nfcore -%}before_text{%- else %}""{%- endif %},
+        {% if is_nfcore -%}after_text{%- else %}""{%- endif %},
+        command
     )
-    {% if is_nfcore -%}log.info(after_text){%- endif %}
     {%- endif %}
 
     //

diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config