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Merge pull request #555 from nf-core/dev
Release 2.1.0
2 parents 1489b71 + 4237c6d commit c7a6f38

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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/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/raredisease'
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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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# TODO nf-core: You can customise AWS full pipeline tests as required
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# Add full size test data (but still relatively small datasets for few samples)
@@ -33,7 +33,7 @@ jobs:
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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/raredisease'
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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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- "-profile test_one_sample,docker"
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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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pull_request:
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types:
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- opened
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- edited
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- synchronize
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branches:
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- master
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pull_request_target:
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runs-on: ubuntu-latest
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steps:
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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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- 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@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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- uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
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with:
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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

‎.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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with:
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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' ' ' >> $GITHUB_OUTPUT
15+
echo "topics=$(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

‎.nf-core.yml

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- docs/images/nf-core-raredisease_logo_dark.png
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- docs/images/nf-core-raredisease_logo_light.png
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- assets/nf-core-raredisease_logo_light.png
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modules_config: False
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repository_type: pipeline
12+
nf_core_version: "2.14.1"

‎.pre-commit-config.yaml

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@@ -3,6 +3,9 @@ repos:
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rev: "v3.1.0"
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hooks:
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- id: prettier
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additional_dependencies:
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- prettier@3.2.5
8+
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- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
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rev: "2.7.3"
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hooks:

‎CHANGELOG.md

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33
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
55

6+
## 2.1.0 - Obelix [2024-05-29]
7+
8+
### `Added`
9+
10+
- A new aligner, bwameme [#553](https://github.com/nf-core/raredisease/pull/553)
11+
- A new parameter `run_mt_for_wes` to turn on mitochondrial analysis for targeted analysis [#552](https://github.com/nf-core/raredisease/pull/552)
12+
- A new parameter `bwa_as_fallback` to switch aligner to bwa in case bwamem2 fails [#551](https://github.com/nf-core/raredisease/pull/551)
13+
- A new parameter `skip_me_calling` to skip mobile element calling and the subsequent annotation of them [#556](https://github.com/nf-core/raredisease/pull/556)
14+
15+
### `Changed`
16+
17+
- Changed valid values for sex according to the PED file format [#550](https://github.com/nf-core/raredisease/pull/550)
18+
- Refactored config files [#538](https://github.com/nf-core/raredisease/pull/538)
19+
- Refactored mobile element annotation subworkflow files [#538](https://github.com/nf-core/raredisease/pull/538)
20+
- Refactored to remove "a process is defined more than once" warning [#557](https://github.com/nf-core/raredisease/pull/557)
21+
- Updated modules [#558](https://github.com/nf-core/raredisease/pull/558)
22+
23+
### `Fixed`
24+
25+
- Include multiallelic indel sites in CADD scoring jobs [#545](https://github.com/nf-core/raredisease/pull/545)
26+
- Fixed issues with samtools merge not being run on samples sequenced over multiple lanes [#538](https://github.com/nf-core/raredisease/pull/538)
27+
- Fixed join issues in the mobile element calling subworkflow which occured when mobile_element_references were not provided [#556](https://github.com/nf-core/raredisease/pull/556)
28+
29+
### Parameters
30+
31+
| Old parameter | New parameter |
32+
| ------------- | --------------- |
33+
| | bwameme |
34+
| | bwa_as_fallback |
35+
| | run_mt_for_wes |
36+
| | skip_me_calling |
37+
38+
:::note
39+
Parameter has been updated if both old and new parameter information is present.
40+
Parameter has been added if just the new parameter information is present.
41+
Parameter has been removed if new parameter information isn't present.
42+
:::
43+
44+
### Module updates
45+
46+
| Tool | Old version | New version |
47+
| -------- | ----------- | ----------- |
48+
| bwa | 0.7.17 | 0.7.18 |
49+
| CADD | 1.6.1 | 1.6.post1 |
50+
| Sentieon | 202308.01 | 202308.02 |
51+
| bwameme | | 1.0.6 |
52+
53+
:::note
54+
Version has been updated if both old and new version information is present.
55+
Version has been added if just the new version information is present.
56+
Version has been removed if new version information isn't present.
57+
:::
58+
659
## 2.0.1 - Asterix (Patch) [2024-03-25]
760

861
### `Fixed`

‎README.md

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[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
1515
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
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[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
17-
[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/raredisease)
17+
[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)
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[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
2020

‎assets/multiqc_config.yml

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33
custom_logo_title: "nf-core/raredisease"
44

55
report_comment: >
6-
This report has been generated by the <a href="https://github.com/nf-core/raredisease/releases/tag/2.0.1" target="_blank">nf-core/raredisease</a>
6+
This report has been generated by the <a href="https://github.com/nf-core/raredisease/releases/tag/2.1.0" target="_blank">nf-core/raredisease</a>
77
analysis pipeline. For information about how to interpret these results, please see the
8-
<a href="https://nf-co.re/raredisease/2.0.1/docs/output" target="_blank">documentation</a>.
8+
<a href="https://nf-co.re/raredisease/2.1.0/docs/output" target="_blank">documentation</a>.
99
report_section_order:
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"nf-core-raredisease-methods-description":
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order: -1000

‎assets/schema_input.json

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]
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},
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"sex": {
43-
"type": "integer",
43+
"type": "string",
4444
"meta": ["sex"],
45-
"enum": [0, 1, 2],
45+
"enum": ["1", "2", "other"],
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"errorMessage": "Sex must be provided and cannot contain spaces"
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},
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"phenotype": {

‎conf/base.config

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errorStrategy = 'retry'
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maxRetries = 2
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}
60-
withName:CUSTOM_DUMPSOFTWAREVERSIONS {
61-
cache = false
60+
withName: 'NFCORE_RAREDISEASE:RAREDISEASE:.*' {
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publishDir = [
62+
enabled: false
63+
]
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}
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}

‎conf/modules/align.config

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*/
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process{
15-
withName: '.*ALIGN:.*' {
15+
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withName: '.*ALIGN:FASTP' {
17+
ext.args = { [
18+
params.min_trimmed_length ? "--length_required ${params.min_trimmed_length}" : '',
19+
'--correction',
20+
'--overrepresentation_analysis'
21+
].join(' ').trim() }
1622
publishDir = [
17-
enabled: false
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path: { "${params.outdir}/trimming" },
24+
mode: params.publish_dir_mode,
25+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
1826
]
1927
}
2028

21-
if (!params.skip_fastp) {
22-
withName: '.*ALIGN:FASTP' {
23-
ext.args = { [
24-
params.min_trimmed_length ? "--length_required ${params.min_trimmed_length}" : '',
25-
'--correction',
26-
'--overrepresentation_analysis'
27-
].join(' ').trim() }
28-
publishDir = [
29-
path: { "${params.outdir}/trimming" },
30-
mode: params.publish_dir_mode,
31-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
32-
]
33-
}
34-
}
35-
36-
if (params.save_mapped_as_cram) {
37-
withName: '.*ALIGN:SAMTOOLS_VIEW' {
38-
ext.args = { '--output-fmt cram --write-index' }
39-
ext.prefix = { "${meta.id}_sorted_md" }
40-
publishDir = [
41-
path: { "${params.outdir}/alignment" },
42-
mode: params.publish_dir_mode,
43-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
44-
]
45-
}
29+
withName: '.*ALIGN:SAMTOOLS_VIEW' {
30+
ext.args = { '--output-fmt cram --write-index' }
31+
ext.prefix = { "${meta.id}_sorted_md" }
32+
publishDir = [
33+
path: { "${params.outdir}/alignment" },
34+
mode: params.publish_dir_mode,
35+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
36+
]
4637
}
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}

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