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Merge pull request #499 from nf-core/dev
1.1.8 Patch Release
2 parents f1e6153 + e21b3ed commit 5d3ee55

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‎.editorconfig‎

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@@ -28,10 +28,6 @@ indent_style = unset
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[/assets/email*]
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indent_size = unset
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# ignore Readme
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[README.md]
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indent_style = unset
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# ignore python
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# ignore python and markdown
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[*.{py,md}]
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indent_style = unset

‎.github/PULL_REQUEST_TEMPLATE.md‎

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@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/taxp
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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/taxprofiler/tree/master/.github/CONTRIBUTING.md)
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- [ ] If necessary, also make a PR on the nf-core/taxprofiler _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
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- [ ] Make sure your code lints (`nf-core lint`).
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- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
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- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
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- [ ] Usage Documentation in `docs/usage.md` is updated.
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- [ ] Output Documentation in `docs/output.md` is updated.

‎.github/workflows/awsfulltest.yml‎

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types: [published]
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workflow_dispatch:
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jobs:
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run-tower:
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run-platform:
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name: Run AWS full tests
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if: github.repository == 'nf-core/taxprofiler'
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runs-on: ubuntu-latest
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steps:
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- name: Launch workflow via tower
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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:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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- uses: actions/upload-artifact@v4
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with:
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name: Tower debug log file
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name: Seqera Platform debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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seqera_platform_action_*.log
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seqera_platform_action_*.json

‎.github/workflows/awstest.yml‎

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@@ -5,13 +5,13 @@ name: nf-core AWS test
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on:
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workflow_dispatch:
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jobs:
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run-tower:
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run-platform:
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name: Run AWS tests
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if: github.repository == 'nf-core/taxprofiler'
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runs-on: ubuntu-latest
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steps:
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# Launch workflow using Tower CLI tool action
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- name: Launch workflow via tower
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# Launch workflow using Seqera Platform CLI tool action
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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:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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- uses: actions/upload-artifact@v4
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with:
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name: Tower debug log file
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name: Seqera Platform debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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seqera_platform_action_*.log
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seqera_platform_action_*.json

‎.github/workflows/ci.yml‎

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steps:
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- name: Check out pipeline code
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uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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uses: nf-core/setup-nextflow@v2
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with:
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version: "${{ matrix.NXF_VER }}"
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‎.github/workflows/download_pipeline.yml‎

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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v2
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- name: Disk space cleanup
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uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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with:
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python-version: "3.12"
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architecture: "x64"
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- name: Inspect download
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run: tree ./${{ env.REPOTITLE_LOWERCASE }}
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- name: Run the downloaded pipeline
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- name: Run the downloaded pipeline (stub)
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id: stub_run_pipeline
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continue-on-error: true
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env:
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NXF_SINGULARITY_CACHEDIR: ./
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NXF_SINGULARITY_HOME_MOUNT: true
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run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
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- name: Run the downloaded pipeline (stub run not supported)
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id: run_pipeline
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if: ${{ job.steps.stub_run_pipeline.status == failure() }}
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env:
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NXF_SINGULARITY_CACHEDIR: ./
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NXF_SINGULARITY_HOME_MOUNT: true
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run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test_nothing,singularity --outdir ./results
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run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results

‎.github/workflows/fix-linting.yml‎

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runs-on: ubuntu-latest
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steps:
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# Use the @nf-core-bot token to check out so we can push later
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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with:
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token: ${{ secrets.nf_core_bot_auth_token }}
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GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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# Install and run pre-commit
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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with:
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python-version: 3.11
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python-version: "3.12"
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- name: Install pre-commit
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run: pip install pre-commit

‎.github/workflows/linting.yml‎

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pre-commit:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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- name: Set up Python 3.11
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uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- name: Set up Python 3.12
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uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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with:
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python-version: 3.11
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cache: "pip"
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python-version: "3.12"
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- name: Install pre-commit
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run: pip install pre-commit
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runs-on: ubuntu-latest
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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uses: nf-core/setup-nextflow@v2
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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with:
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python-version: "3.11"
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python-version: "3.12"
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architecture: "x64"
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- name: Install dependencies
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- name: Upload linting log file artifact
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if: ${{ always() }}
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uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
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uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
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name: linting-logs
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path: |

‎.github/workflows/linting_comment.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Download lint results
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uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
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uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
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with:
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workflow: linting.yml
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workflow_conclusion: completed

‎.github/workflows/release-announcements.yml‎

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- name: get topics and convert to hashtags
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id: get_topics
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run: |
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curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
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echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT
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- uses: rzr/fediverse-action@master
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with:
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Please see the changelog: ${{ github.event.release.html_url }}
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${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
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${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
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send-tweet:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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with:
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python-version: "3.10"
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- name: Install dependencies

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