Important! Template update for nf-core/tools v3.1.0

.github/CONTRIBUTING.md

@@ -1,23 +1,23 @@
-# nf-core/plantpathsurveil: Contributing Guidelines
+# `nf-core/pathogensurveillance`: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving nf-core/plantpathsurveil.
+Many thanks for taking an interest in improving nf-core/pathogensurveillance.
 
-We try to manage the required tasks for nf-core/plantpathsurveil using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for nf-core/pathogensurveillance using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
 > [!NOTE]
-> If you need help using or modifying nf-core/plantpathsurveil then the best place to ask is on the nf-core Slack [#plantpathsurveil](https://nfcore.slack.com/channels/plantpathsurveil) channel ([join our Slack here](https://nf-co.re/join/slack)).
+> If you need help using or modifying nf-core/pathogensurveillance then the best place to ask is on the nf-core Slack [#pathogensurveillance](https://nfcore.slack.com/channels/pathogensurveillance) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
 
-If you'd like to write some code for nf-core/plantpathsurveil, the standard workflow is as follows:
+If you'd like to write some code for nf-core/pathogensurveillance, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/plantpathsurveil issues](https://github.com/nf-core/plantpathsurveil/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/plantpathsurveil repository](https://github.com/nf-core/plantpathsurveil) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [nf-core/pathogensurveillance issues](https://github.com/nf-core/pathogensurveillance/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/pathogensurveillance repository](https://github.com/nf-core/pathogensurveillance) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
@@ -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/plantpathsurveil documentation](https://nf-co.re/plantpathsurveil/usage) and don't hesitate to get in touch on the nf-core Slack [#plantpathsurveil](https://nfcore.slack.com/channels/plantpathsurveil) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [nf-core/pathogensurveillance documentation](https://nf-co.re/pathogensurveillance/usage) and don't hesitate to get in touch on the nf-core Slack [#pathogensurveillance](https://nfcore.slack.com/channels/pathogensurveillance) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Pipeline contribution conventions
 
-To make the nf-core/plantpathsurveil 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/pathogensurveillance` 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`.
 
@@ -115,7 +115,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/nf-core/plantpathsurveil/codespaces)
+- Open the repo in [Codespaces](https://github.com/nf-core/pathogensurveillance/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -8,7 +8,7 @@ body:
         Before you post this issue, please check the documentation:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-        - [nf-core/plantpathsurveil pipeline documentation](https://nf-co.re/plantpathsurveil/usage)
+        - [nf-core/pathogensurveillance pipeline documentation](https://nf-co.re/pathogensurveillance/usage)
 
   - type: textarea
     id: description
@@ -47,4 +47,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of nf-core/plantpathsurveil _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of nf-core/pathogensurveillance _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/config.yml

@@ -2,6 +2,6 @@ contact_links:
   - name: Join nf-core
     url: https://nf-co.re/join
     about: Please join the nf-core community here
-  - name: "Slack #plantpathsurveil channel"
-    url: https://nfcore.slack.com/channels/plantpathsurveil
-    about: Discussion about the nf-core/plantpathsurveil pipeline
+  - name: "Slack #pathogensurveillance channel"
+    url: https://nfcore.slack.com/channels/pathogensurveillance
+    about: Discussion about the nf-core/pathogensurveillance pipeline

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the nf-core/plantpathsurveil pipeline
+description: Suggest an idea for the nf-core/pathogensurveillance pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,22 +1,22 @@
 <!--
-# nf-core/plantpathsurveil pull request
+# nf-core/pathogensurveillance pull request
 
-Many thanks for contributing to nf-core/plantpathsurveil!
+Many thanks for contributing to nf-core/pathogensurveillance!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/plantpathsurveil/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/pathogensurveillance/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/plantpathsurveil/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the nf-core/plantpathsurveil _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/pathogensurveillance/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the nf-core/pathogensurveillance _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

.github/workflows/awsfulltest.yml

@@ -1,11 +1,12 @@
 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/master 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:
+      - main
       - master
   workflow_dispatch:
   pull_request_review:
@@ -15,21 +16,33 @@ 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/plantpathsurveil' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    if: github.repository == 'nf-core/pathogensurveillance' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || 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 }}'
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
           test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
@@ -40,11 +53,11 @@ jobs:
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/plantpathsurveil/work-${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/pathogensurveillance/work-${{ github.sha }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/plantpathsurveil/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/pathogensurveillance/results-${{ github.sha }}"
             }
           profiles: test_full
 

.github/workflows/awstest.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   run-platform:
     name: Run AWS tests
-    if: github.repository == 'nf-core/plantpathsurveil'
+    if: github.repository == 'nf-core/pathogensurveillance'
     runs-on: ubuntu-latest
     steps:
       # Launch workflow using Seqera Platform CLI tool action
@@ -18,10 +18,10 @@ jobs:
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/plantpathsurveil/work-${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/pathogensurveillance/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/plantpathsurveil/results-test-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/pathogensurveillance/results-test-${{ github.sha }}"
             }
           profiles: test
 

.github/workflows/branch.yml

@@ -1,19 +1,21 @@
 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`/`master` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches:
+      - main
+      - master
 
 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/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'nf-core/plantpathsurveil'
+        if: github.repository == 'nf-core/pathogensurveillance'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/plantpathsurveil ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/pathogensurveillance ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
@@ -22,7 +24,7 @@ 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 +34,9 @@ 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

@@ -22,7 +22,7 @@ jobs:
   test:
     name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/plantpathsurveil') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/pathogensurveillance') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -45,7 +45,7 @@ jobs:
             profile: "singularity"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2

.github/workflows/download_pipeline.yml

@@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
-#  - when a PR is opened or reopened to master branch
+#  - when a PR is opened or reopened to main/master branch
 #  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
 on:
   workflow_dispatch:
@@ -17,9 +17,11 @@ on:
       - edited
       - synchronize
     branches:
+      - main
       - master
   pull_request_target:
     branches:
+      - main
       - master
 
 env:
@@ -35,7 +37,7 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
@@ -69,7 +71,7 @@ jobs:
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
           --container-cache-utilisation 'amend' \
           --download-configuration 'yes'