STRY0019104 - Test against GSP version of Nextflow in GitHub CI for all pipelines

.github/workflows/branch.yml

@@ -1,6 +1,6 @@
 name: nf-core branch protection
 # This workflow is triggered on PRs to `main`/`master` branch on the repository
-# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
+# It fails when someone tries to make a PR against the phac-nml `main`/`master` branch instead of `dev`
 on:
   pull_request_target:
     branches:
@@ -11,7 +11,7 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the phac-nml repo main/master branch are only ok if coming from the phac-nml repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'phac-nml/iridanextexample2'
         run: |
@@ -35,7 +35,7 @@ jobs:
             Hi @${{ github.event.pull_request.user.login }},
 
             It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
-            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
+            The ${{github.event.pull_request.base.ref}} branch on phac-nml repositories should always contain code from the latest release.
             Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.

.github/workflows/linting.yml

@@ -1,4 +1,4 @@
-name: nf-core linting of iridanextexample2
+name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
 # It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
@@ -50,15 +50,15 @@ jobs:
           pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'main' }}
+        if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
-        if: ${{ github.base_ref == 'main' }}
+        if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/nf-test.yml

@@ -68,15 +68,15 @@ jobs:
         shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
         profile: [conda, docker, singularity]
         isMain:
-          - ${{ github.base_ref == 'main' || github.base_ref == 'master' }}
+          - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         # Exclude conda and singularity on dev
         exclude:
           - isMain: false
             profile: "conda"
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.10.5"
+          - "24.10.3"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
@@ -93,6 +93,7 @@ jobs:
         continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+          NXF_VERSION: ${{ matrix.NXF_VER }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}

.github/workflows/template-version-comment.yml

@@ -0,0 +1,46 @@
+name: nf-core template version comment
+# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
+# It posts a comment to the PR, even if it comes from a fork.
+
+on: pull_request_target
+
+jobs:
+  template_version:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Read template version from .nf-core.yml
+        uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
+      - name: Install nf-core
+        run: |
+          python -m pip install --upgrade pip
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Check nf-core outdated
+        id: nf_core_outdated
+        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
+
+      - name: Post nf-core template version comment
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        if: |
+          contains(env.OUTPUT, 'nf-core')
+        with:
+          repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
+          allow-repeats: false
+          message: |
+            > [!WARNING]
+            > Newer version of the nf-core template is available.
+            >
+            > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            > Please update your pipeline to the latest version.
+            >
+            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+          #

.nf-core.yml

@@ -3,7 +3,6 @@ repository_type: pipeline
 nf_core_version: 3.3.2
 
 lint:
-  included_configs: False
   files_unchanged:
     - CODE_OF_CONDUCT.md
     - assets/nf-core-iridanextexample2_logo_light.png
@@ -12,15 +11,14 @@ lint:
     - .github/ISSUE_TEMPLATE/bug_report.yml
     - .github/CONTRIBUTING.md
     - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/linting.yml
+    - .github/workflows/branch.yml
     - assets/email_template.txt
     - docs/README.md
-    - .github/workflows/linting.yml
   nextflow_config:
     - custom_config
     - manifest.name
     - manifest.homePage
-    - validation.help.beforeText
-    - validation.help.afterText
     - validation.summary.beforeText
     - validation.summary.afterText
   multiqc_config:

CHANGELOG.md

@@ -3,6 +3,18 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+
+### `Added`
+
+- Adding GitHub CI tests against Nextflow `24.10.3`. [PR #8](https://github.com/phac-nml/iridanextexample2/pull/8)
+  - Required downgrading minimum Nextflow version from `24.10.5` to `24.10.3`.
+
+### `Updated`
+
+- Some minor updates to GitHub actions and `.nf-core.yml` to better match latest nf-core template. [PR #8](https://github.com/phac-nml/iridanextexample2/pull/8)
+- Updated nf-core modules and subworkflows. [PR #8](https://github.com/phac-nml/iridanextexample2/pull/8)
+
 ## [0.1.0] - 2025-07-25
 
 - Initial release of phac-nml/iridanextexample2, created with the [nf-core](https://nf-co.re/) template.

README.md

@@ -4,8 +4,7 @@
 [![GitHub Actions Linting Status](https://github.com/phac-nml/iridanextexample2/actions/workflows/linting.yml/badge.svg)](https://github.com/phac-nml/iridanextexample2/actions/workflows/linting.yml)
 [![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/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.3-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
 [![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/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

main.nf

@@ -69,10 +69,15 @@ workflow {
     PIPELINE_INITIALISATION (
         params.version,
         params.validate_params,
-        params.monochrome_logs,
         args,
         params.outdir,
-        params.input
+        params.input,
+        params.help,
+        params.help_full,
+        params.show_hidden,
+        "",
+        "",
+        "nextflow run phac-nml/iridanextexample2 -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
     )
 
     //

modules.json

@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
                         "installed_by": ["modules"]
                     }
                 }
@@ -21,17 +21,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
+                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
                         "installed_by": ["subworkflows"]
                     }
                 }

nextflow.config

@@ -259,7 +259,7 @@ manifest {
     description     = """An example pipeline for running on IRIDA-Next with nf-schema"""
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
-    nextflowVersion = '!>=24.10.5'
+    nextflowVersion = '!>=24.10.3'
     version         = '0.1.0'
     doi             = ''
 }
@@ -269,7 +269,9 @@ plugins {
     id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
     id 'nf-iridanext@0.3.0'
 }
+
 includeConfig 'conf/iridanext.config'
+
 validation {
     defaultIgnoreParams = ["genomes"]
     monochromeLogs = params.monochrome_logs
@@ -278,6 +280,8 @@ validation {
         command = "nextflow run phac-nml/iridanextexample2 -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
+        beforeText = ""
+        afterText = ""
     }
 }