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Merge pull request #563 from nf-core/dev
v1.2.2 - Bouncy Basenji Patch PR
2 parents 0af416a + 320f6f2 commit 80d2fcc

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.editorconfig

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@@ -31,3 +31,7 @@ indent_size = unset
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# ignore python and markdown
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[*.{py,md}]
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indent_style = unset
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# ignore ro-crate metadata files
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[**/ro-crate-metadata.json]
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insert_final_newline = unset

.github/CONTRIBUTING.md

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@@ -1,4 +1,4 @@
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# nf-core/taxprofiler: Contributing Guidelines
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# `nf-core/taxprofiler`: Contributing Guidelines
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Hi there!
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Many thanks for taking an interest in improving nf-core/taxprofiler.
@@ -55,23 +55,23 @@ These tests are run both with the latest available version of `Nextflow` and als
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:warning: Only in the unlikely and regretful event of a release happening with a bug.
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58-
- On your own fork, make a new branch `patch` based on `upstream/master`.
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- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
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- Fix the bug, and bump version (X.Y.Z+1).
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- A PR should be made on `master` from patch to directly this particular bug.
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- Open a pull-request from `patch` to `main`/`master` with the changes.
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## Getting help
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For further information/help, please consult the [nf-core/taxprofiler documentation](https://nf-co.re/taxprofiler/usage) and don't hesitate to get in touch on the nf-core Slack [#taxprofiler](https://nfcore.slack.com/channels/taxprofiler) channel ([join our Slack here](https://nf-co.re/join/slack)).
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## Pipeline contribution conventions
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To make the nf-core/taxprofiler 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.
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To make the `nf-core/taxprofiler` 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.
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### Adding a new step
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If you wish to contribute a new step, please use the following coding standards:
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1. Define the corresponding input channel into your new process from the expected previous process channel
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1. Define the corresponding input channel into your new process from the expected previous process channel.
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2. Write the process block (see below).
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3. Define the output channel if needed (see below).
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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:
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### Default values
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Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
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Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
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Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
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.github/ISSUE_TEMPLATE/bug_report.yml

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

.github/workflows/awsfulltest.yml

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@@ -1,11 +1,12 @@
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name: nf-core AWS full size tests
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# This workflow is triggered on PRs opened against the master branch.
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# This workflow is triggered on PRs opened against the main/master branch.
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# It can be additionally triggered manually with GitHub actions workflow dispatch button.
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# It runs the -profile 'test_full' on AWS batch
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on:
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pull_request:
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branches:
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- main
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- master
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workflow_dispatch:
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pull_request_review:
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if: github.repository == 'nf-core/taxprofiler' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
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runs-on: ubuntu-latest
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steps:
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- uses: octokit/[email protected]
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- name: Get PR reviews
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uses: octokit/[email protected]
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if: github.event_name != 'workflow_dispatch'
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id: check_approvals
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continue-on-error: true
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with:
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route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
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route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- id: test_variables
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- name: Check for approvals
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if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
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run: |
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echo "No review approvals found. At least 2 approvals are required to run this action automatically."
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exit 1
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- name: Check for enough approvals (>=2)
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id: test_variables
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if: github.event_name != 'workflow_dispatch'
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run: |
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JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
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CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
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test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
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- name: Launch workflow via Seqera Platform
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uses: seqeralabs/action-tower-launch@v2
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with:

.github/workflows/branch.yml

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name: nf-core branch protection
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# This workflow is triggered on PRs to master branch on the repository
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# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
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# This workflow is triggered on PRs to `main`/`master` branch on the repository
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# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
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on:
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pull_request_target:
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branches: [master]
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branches:
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- main
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- master
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jobs:
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test:
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runs-on: ubuntu-latest
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steps:
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# PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
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# PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
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- name: Check PRs
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if: github.repository == 'nf-core/taxprofiler'
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run: |
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uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
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with:
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message: |
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## This PR is against the `master` branch :x:
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## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
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* Do not close this PR
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* Click _Edit_ and change the `base` to `dev`
@@ -32,9 +34,9 @@ jobs:
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Hi @${{ github.event.pull_request.user.login }},
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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.
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The `master` branch on nf-core repositories should always contain code from the latest release.
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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.
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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.
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The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
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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.
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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.
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Note that even after this, the test will continue to show as failing until you push a new commit.

.github/workflows/ci.yml

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profile: "singularity"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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- name: Set up Nextflow
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uses: nf-core/setup-nextflow@v2
@@ -100,7 +100,7 @@ jobs:
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echo "motus,db1_mOTU,,short,db_mOTU" >> 'database_motus.csv'
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echo "motus,db2_mOTU,,long,db_mOTU" >> 'database_motus.csv'
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echo "motus,db3_mOTU,,short;long,db_mOTU" >> 'database_motus.csv'
103-
nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.test_name }} --databases ./database_motus.csv --outdir ./results_${{ matrix.test_name }};
103+
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},${{ matrix.test_name }} --databases ./database_motus.csv --outdir ./results_${{ matrix.test_name }};
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else
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nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.test_name }} --outdir ./results_${{ matrix.test_name }};
105+
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},${{ matrix.test_name }} --outdir ./results_${{ matrix.test_name }};
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fi

.github/workflows/download_pipeline.yml

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33
# Run the workflow when:
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# - dispatched manually
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# - when a PR is opened or reopened to master branch
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# - when a PR is opened or reopened to main/master branch
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# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
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on:
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workflow_dispatch:
@@ -17,25 +17,42 @@ on:
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- edited
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- synchronize
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branches:
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- main
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- master
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pull_request_target:
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branches:
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- main
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- master
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env:
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NXF_ANSI_LOG: false
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jobs:
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configure:
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runs-on: ubuntu-latest
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outputs:
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REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
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REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
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REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
37+
steps:
38+
- name: Get the repository name and current branch
39+
id: get_repo_properties
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run: |
41+
echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
42+
echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
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echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
44+
2945
download:
3046
runs-on: ubuntu-latest
47+
needs: configure
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steps:
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- name: Install Nextflow
3350
uses: nf-core/setup-nextflow@v2
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3552
- name: Disk space cleanup
3653
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
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38-
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
55+
- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
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with:
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python-version: "3.12"
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architecture: "x64"
@@ -50,12 +67,6 @@ jobs:
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python -m pip install --upgrade pip
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pip install git+https://github.com/nf-core/tools.git@dev
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- name: Get the repository name and current branch set as environment variable
54-
run: |
55-
echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
56-
echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
57-
echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
58-
5970
- name: Make a cache directory for the container images
6071
run: |
6172
mkdir -p ./singularity_container_images
@@ -64,55 +75,59 @@ jobs:
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env:
6576
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
6677
run: |
67-
nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
68-
--revision ${{ env.REPO_BRANCH }} \
69-
--outdir ./${{ env.REPOTITLE_LOWERCASE }} \
78+
nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
79+
--revision ${{ needs.configure.outputs.REPO_BRANCH }} \
80+
--outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \
7081
--compress "none" \
7182
--container-system 'singularity' \
72-
--container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
83+
--container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
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--container-cache-utilisation 'amend' \
7485
--download-configuration 'yes'
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- name: Inspect download
77-
run: tree ./${{ env.REPOTITLE_LOWERCASE }}
88+
run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
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90+
- name: Inspect container images
91+
run: tree ./singularity_container_images | tee ./container_initial
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- name: Count the downloaded number of container images
8094
id: count_initial
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run: |
8296
image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
8397
echo "Initial container image count: $image_count"
84-
echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
98+
echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT"
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- name: Run the downloaded pipeline (stub)
87101
id: stub_run_pipeline
88102
continue-on-error: true
89103
env:
90104
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
91105
NXF_SINGULARITY_HOME_MOUNT: true
92-
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
106+
run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
93107
- name: Run the downloaded pipeline (stub run not supported)
94108
id: run_pipeline
95-
if: ${{ job.steps.stub_run_pipeline.status == failure() }}
109+
if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}
96110
env:
97111
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
98112
NXF_SINGULARITY_HOME_MOUNT: true
99-
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
113+
run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results
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101115
- name: Count the downloaded number of container images
102116
id: count_afterwards
103117
run: |
104118
image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
105119
echo "Post-pipeline run container image count: $image_count"
106-
echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
120+
echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
107121
108122
- name: Compare container image counts
109123
run: |
110-
if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
111-
initial_count=${{ env.IMAGE_COUNT_INITIAL }}
112-
final_count=${{ env.IMAGE_COUNT_AFTER }}
124+
if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
125+
initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
126+
final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
113127
difference=$((final_count - initial_count))
114128
echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
115-
tree ./singularity_container_images
129+
tree ./singularity_container_images > ./container_afterwards
130+
diff ./container_initial ./container_afterwards
116131
exit 1
117132
else
118133
echo "The pipeline can be downloaded successfully!"

.github/workflows/fix-linting.yml

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runs-on: ubuntu-latest
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steps:
1515
# Use the @nf-core-bot token to check out so we can push later
16-
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
16+
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
1717
with:
1818
token: ${{ secrets.nf_core_bot_auth_token }}
1919

@@ -32,7 +32,7 @@ jobs:
3232
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
3333

3434
# Install and run pre-commit
35-
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
35+
- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
3636
with:
3737
python-version: "3.12"
3838

.github/workflows/linting.yml

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@@ -14,10 +14,10 @@ jobs:
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pre-commit:
1515
runs-on: ubuntu-latest
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steps:
17-
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
17+
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
1818

1919
- name: Set up Python 3.12
20-
uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
20+
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
2121
with:
2222
python-version: "3.12"
2323

@@ -31,12 +31,12 @@ jobs:
3131
runs-on: ubuntu-latest
3232
steps:
3333
- name: Check out pipeline code
34-
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
34+
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
3535

3636
- name: Install Nextflow
3737
uses: nf-core/setup-nextflow@v2
3838

39-
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
39+
- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
4040
with:
4141
python-version: "3.12"
4242
architecture: "x64"
@@ -74,7 +74,7 @@ jobs:
7474

7575
- name: Upload linting log file artifact
7676
if: ${{ always() }}
77-
uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
77+
uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
7878
with:
7979
name: linting-logs
8080
path: |

.github/workflows/linting_comment.yml

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@@ -11,7 +11,7 @@ jobs:
1111
runs-on: ubuntu-latest
1212
steps:
1313
- name: Download lint results
14-
uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
14+
uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
1515
with:
1616
workflow: linting.yml
1717
workflow_conclusion: completed

.github/workflows/release-announcements.yml

+1-1
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@@ -31,7 +31,7 @@ jobs:
3131
runs-on: ubuntu-latest
3232

3333
steps:
34-
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
34+
- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
3535
with:
3636
python-version: "3.10"
3737
- name: Install dependencies

.github/workflows/template_version_comment.yml

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@@ -9,7 +9,7 @@ jobs:
99
runs-on: ubuntu-latest
1010
steps:
1111
- name: Check out pipeline code
12-
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
12+
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
1313
with:
1414
ref: ${{ github.event.pull_request.head.sha }}
1515

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