nf-core · nvnieuwk · Sep 10, 2025 · Sep 2, 2025 · Sep 2, 2025 · Sep 2, 2025
diff --git a/.github/snapshots/default.nf.test.snap b/.github/snapshots/default.nf.test.snap
@@ -107,7 +107,7 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.0"
         },
         "timestamp": "2025-05-07T13:29:04.284923"
     }

diff --git a/.github/snapshots/gpu.nf.test.snap b/.github/snapshots/gpu.nf.test.snap
@@ -107,7 +107,7 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.0"
         },
         "timestamp": "2025-06-16T14:29:10.076573"
     }

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -32,7 +32,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "24.10.5"
+          - "25.04.0"
           - "latest-everything"
     steps:
       - name: go to subdirectory and change nextflow workdir

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -32,7 +32,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "24.10.5"
+          - "25.04.0"
           - "latest-everything"
     steps:
       - name: go to working directory

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,8 @@
 ### Template
 
 - Update the `download_pipeline` workflow to remove dependency on `dev` branch of tools ([#3734](https://github.com/nf-core/tools/pull/3734))
+- Bump nf-schema to 2.5.0 and update the help message creation to be compatible with future Nextflow versions ([#3743](https://github.com/nf-core/tools/pull/3743))
+- Bump minimum Nextflow version to 25.04.0 ([#3743](https://github.com/nf-core/tools/pull/3743))
 
 ### Linting
 

diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml
@@ -80,7 +80,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.10.5"
+          - "25.04.0"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
@@ -20,7 +20,7 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![nf-core template version](https://img.shields.io/badge/nf--core_template-{{ nf_core_version }}-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/{{ nf_core_version }})
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
@@ -82,7 +82,10 @@ workflow {
         params.monochrome_logs,
         args,
         params.outdir,
-        params.input
+        params.input{% if nf_schema %},
+        params.help,
+        params.help_full,
+        params.show_hidden{% endif %}
     )
     {%- endif %}
 

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
@@ -220,7 +220,12 @@ profiles {
     test_full { includeConfig 'conf/test_full.config' }
     {%- endif %}
 }
+{%- if igenomes %}
 
+// Set AWS client to anonymous when using the default igenomes_base
+aws.client.anonymous = !params.igenomes_ignore && params.igenomes_base?.startsWith('s3://ngi-igenomes/igenomes/') ?: false
+
+{%- endif %}
 {% if nf_core_configs -%}
 // Load nf-core custom profiles from different institutions
 
@@ -308,48 +313,20 @@ manifest {
     description     = """{{ description }}"""
     mainScript      = 'main.nf'
     defaultBranch   = '{{ default_branch }}'
-    nextflowVersion = '!>=24.10.5'
+    nextflowVersion = '!>=25.04.0'
     version         = '{{ version }}'
     doi             = ''
 }
 
 {% if nf_schema -%}
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.4.2' // 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
 }
 
 validation {
     defaultIgnoreParams = ["genomes"]
     monochromeLogs = params.monochrome_logs
-    help {
-        enabled = true
-        command = "nextflow run {{ name }} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-        fullParameter = "help_full"
-        showHiddenParameter = "show_hidden"
-        {%- if is_nfcore %}
-        beforeText = """
--\033[2m----------------------------------------------------\033[0m-
-                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
-\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
-\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
-\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
-                                        \033[0;32m`._,._,\'\033[0m
-\033[0;35m  {{ name }} ${manifest.version}\033[0m
--\033[2m----------------------------------------------------\033[0m-
-"""
-        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
-* The nf-core framework
-    https://doi.org/10.1038/s41587-020-0439-x
-
-* Software dependencies
-    https://github.com/{{ name }}/blob/{{ default_branch }}/CITATIONS.md
-"""{% endif %}
-    }{% if is_nfcore %}
-    summary {
-        beforeText = validation.help.beforeText
-        afterText = validation.help.afterText
-    }{% endif %}
 }
 {%- endif %}
 

diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
@@ -235,7 +235,19 @@
                     "fa_icon": "far calendar",
                     "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
                     "hidden": true
-                }
+                }{% if nf_schema %},
+                "help": {
+                    "type": ["boolean", "string"],
+                    "description": "Display the help message.",
+                },
+                "help_full": {
+                    "type": "boolean",
+                    "description": "Display the full detailed help message.",
+                },
+                "show_hidden": {
+                    "type": "boolean",
+                    "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided).",
+                }{% 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
@@ -10,7 +10,8 @@
 
 {% if nf_schema %}include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
 include { paramsSummaryMap          } from 'plugin/nf-schema'
-include { samplesheetToList         } from 'plugin/nf-schema'{% endif %}
+include { samplesheetToList         } from 'plugin/nf-schema'
+include { paramsHelp                } from 'plugin/nf-schema'{% endif %}
 {%- if email %}
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 {%- endif %}
@@ -36,10 +37,52 @@ workflow PIPELINE_INITIALISATION {
     nextflow_cli_args //   array: List of positional nextflow CLI args
     outdir            //  string: The output directory where the results will be saved
     input             //  string: Path to input samplesheet
+    {% if nf_schema %}help              // boolean: Display help message and exit
+    help_full         // boolean: Show the full help message
+    show_hidden       // boolean: Show hidden parameters in the help message{% endif %}
 
     main:
 
     ch_versions = Channel.empty()
+    {%- if nf_schema %}
+
+    //
+    // Print help message
+    //
+
+    {%- if is_nfcore %}
+    before_text = """
+-\033[2m----------------------------------------------------\033[0m-
+                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
+\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
+\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
+\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
+                                        \033[0;32m`._,._,\'\033[0m
+\033[0;35m  {{ name }} ${workflow.manifest.version}\033[0m
+-\033[2m----------------------------------------------------\033[0m-
+"""
+    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
+* The nf-core framework
+    https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+    https://github.com/{{ name }}/blob/{{ default_branch }}/CITATIONS.md
+"""{% endif %}
+    command = "nextflow run {${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 %}
 
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
@@ -56,11 +99,13 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
+    {% if is_nfcore -%}log.info(before_text){%- endif %}
     UTILS_NFSCHEMA_PLUGIN (
         workflow,
         validate_params,
         null
     )
+    {% if is_nfcore -%}log.info(after_text){%- endif %}
     {%- endif %}
 
     //

diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml
@@ -362,10 +362,6 @@ configurations:
         nextflow_config:
           - "manifest.name"
           - "manifest.homePage"
-          - "validation.help.beforeText"
-          - "validation.help.afterText"
-          - "validation.summary.beforeText"
-          - "validation.summary.afterText"
         multiqc_config:
           - "report_comment"
       nfcore_pipelines: False

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
@@ -183,26 +183,14 @@ def nextflow_config(self) -> dict[str, list[str]]:
 
         if "nf-schema" in found_plugins:
             passed.append("Found nf-schema plugin")
-            if self.nf_config.get("validation.help.enabled", "false") == "false":
-                failed.append(
-                    "The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages"
-                )
-            config_fail.extend([["validation.help.enabled"]])
-            config_warn.extend(
-                [
-                    ["validation.help.beforeText"],
-                    ["validation.help.afterText"],
-                    ["validation.help.command"],
-                    ["validation.summary.beforeText"],
-                    ["validation.summary.afterText"],
-                ]
-            )
             config_fail_ifdefined.extend(
                 [
                     "params.validationFailUnrecognisedParams",
                     "params.validationLenientMode",
                     "params.validationSchemaIgnoreParams",
                     "params.validationShowHiddenParams",
+                    "validation.failUnrecognisedParams",
+                    "validation.failUnrecognisedHeaders",
                 ]
             )
 

diff --git a/nf_core/pipelines/lint/readme.py b/nf_core/pipelines/lint/readme.py
@@ -53,7 +53,7 @@ def readme(self):
 
     if "nextflow_badge" not in ignore_configs:
         # Check that there is a readme badge showing the minimum required version of Nextflow
-        # [![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+        # [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
         # and that it has the correct version
         nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/version-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-green\?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow\.io\)\]\(https://www\.nextflow\.io/\)"
         match = re.search(nf_badge_re, content)