Template update for nf-core/tools version 3.1.1

.editorconfig

@@ -31,3 +31,15 @@ indent_size = unset
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
+
+# ignore ro-crate metadata files
+[**/ro-crate-metadata.json]
+insert_final_newline = unset
+
+# ignore nf-test snapshots
+[*.nf.test.snap]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset

.github/CODEOWNERS

@@ -1 +1 @@
-workflows/sarek/** @nf-core/sarek
+* @maxulysse

.github/CONTRIBUTING.md

@@ -1,4 +1,4 @@
-# nf-core/references: Contributing Guidelines
+# `nf-core/references`: Contributing Guidelines
 
 Hi there!
 Many thanks for taking an interest in improving nf-core/references.
@@ -55,23 +55,23 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-- On your own fork, make a new branch `patch` based on `upstream/master`.
+- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
 - Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+- Open a pull-request from `patch` to `main`/`master` with the changes.
 
 ## Getting help
 
 For further information/help, please consult the [nf-core/references documentation](https://nf-co.re/references/usage) and don't hesitate to get in touch on the nf-core Slack [#references](https://nfcore.slack.com/channels/references) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Pipeline contribution conventions
 
-To make the nf-core/references code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the `nf-core/references` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
 If you wish to contribute a new step, please use the following coding standards:
 
-1. Define the corresponding input channel into your new process from the expected previous process channel
+1. Define the corresponding input channel into your new process from the expected previous process channel.
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
@@ -84,7 +84,7 @@ If you wish to contribute a new step, please use the following coding standards:
 
 ### Default values
 
-Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
 
 Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -9,7 +9,6 @@ body:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
         - [nf-core/references pipeline documentation](https://nf-co.re/references/usage)
-
   - type: textarea
     id: description
     attributes:

.github/workflows/awsfulltest.yml

@@ -1,30 +1,41 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on PRs opened against the master branch.
+# This workflow is triggered on PRs opened against the main branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   pull_request:
     branches:
-      - master
+      - main
   workflow_dispatch:
   pull_request_review:
     types: [submitted]
 
 jobs:
   run-platform:
     name: Run AWS full tests
-    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
-    if: github.repository == 'nf-core/references' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    # run only if the PR is approved by at least 2 reviewers and against the main branch or manually triggered
+    if: github.repository == 'nf-core/references' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'main' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - uses: octokit/[email protected]
+      - name: Get PR reviews
+        uses: octokit/[email protected]
+        if: github.event_name != 'workflow_dispatch'
         id: check_approvals
+        continue-on-error: true
         with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - id: test_variables
+
+      - name: Check for approvals
+        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
+        run: |
+          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
+          exit 1
+
+      - name: Check for enough approvals (>=2)
+        id: test_variables
         if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'

.github/workflows/branch.yml

@@ -1,15 +1,16 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to `main` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches:
+      - main
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/references'
         run: |
@@ -22,7 +23,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +33,9 @@ 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 }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` 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.
+            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.
+            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.
             Note that even after this, the test will continue to show as failing until you push a new commit.

.github/workflows/ci.yml

@@ -19,58 +19,52 @@ env:
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
 concurrency:
-  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref
+    }}"
   cancel-in-progress: true
 
 jobs:
   test:
+    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.filter
+      }} | ${{ matrix.profile }} | ${{ matrix.shard }}/2"
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository
+      == 'nf-core/references') }}"
     runs-on: ubuntu-latest
-    name: "Test ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/2"
     strategy:
       fail-fast: false
       matrix:
         NXF_VER:
-          - "24.10.1"
-          - "latest-everything"
-        filter: ["pipeline"]
-        # filter: ["process", "workflow", "function", "pipeline"]
-        profile: ["conda", "docker", "singularity"]
+          - 24.10.1
+          - latest-everything
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
+        filter:
+          ["pipeline"]
+          # filter: ["process", "workflow", "function", "pipeline"]
         shard: [1, 2]
-        isMaster:
-          - ${{ github.base_ref == 'master' }}
+        isMain:
+          - ${{ github.base_ref == 'main' }}
+        # Exclude conda and singularity on dev
         exclude:
-          - isMaster: false
+          - isMain: false
             profile: "conda"
-          - isMaster: false
+          - isMain: false
             profile: "singularity"
-
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
-        with:
-          distribution: "temurin"
-          java-version: "17"
-
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
-        with:
-          python-version: "3.11"
-          architecture: "x64"
-
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Set up nf-test
-        uses: nf-core/setup-nf-test@v1
-        with:
-          version: ${{ env.NFT_VER }}
-
-      - name: Set up apptainer
+      - name: Set up Apptainer
         if: matrix.profile == 'singularity'
         uses: eWaterCycle/setup-apptainer@main
 
@@ -80,17 +74,12 @@ jobs:
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
-      - name: Cache pdiff
-        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
-        id: cache-pip-pdiff
+      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
         with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-pdiff
-
-      - name: Install pdiff
-        run: python -m pip install --upgrade pip pdiff cryptography
+          python-version: "3.11"
+          architecture: "x64"
 
-      - name: Set up miniconda
+      - name: Set up Miniconda
         if: matrix.profile == 'conda'
         uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
         with:
@@ -105,8 +94,23 @@ jobs:
           echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
           echo $(realpath python) >> $GITHUB_PATH
 
-      - name: Disk space cleanup
-        uses: jlumbroso/[email protected]
+      - name: Set up nf-test
+        uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFT_VER }}
+
+      - name: Cache pdiff
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+        id: cache-pip-pdiff
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-pdiff
+
+      - name: Install pdiff
+        run: python -m pip install --upgrade pip pdiff cryptography
+
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Start summary
         id: print-test
@@ -126,18 +130,19 @@ jobs:
             --filter ${{ matrix.filter }} \
             | grep PASSED | cut -d "'" -f 2 | sed 's/^/- /' | sort -u >> $GITHUB_STEP_SUMMARY
 
-      - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/2"
+      - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard
+          }}/2"
         run: |
           nf-test test \
-              --ci \
-              --debug \
-              --verbose \
-              --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
-              --shard ${{ matrix.shard }}/2 \
-              --changed-since HEAD^ \
-              --follow-dependencies \
-              --profile "+${{ matrix.profile }}" \
-              --filter ${{ matrix.filter }}
+            --ci \
+            --debug \
+            --verbose \
+            --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
+            --shard ${{ matrix.shard }}/2 \
+            --changed-since HEAD^ \
+            --follow-dependencies \
+            --profile "+${{ matrix.profile }}" \
+            --filter ${{ matrix.filter }}
 
       - name: Print success in summary
         if: success()