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TCLamnidisTCLamnidis
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Merge branch 'main' into add-2021_Delser_SciData
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‎.github/workflows/create_package_recipe.yml‎

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types: [created]
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jobs:
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deploy:
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create_recipe:
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# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
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if: >
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contains(github.event.comment.html_url, '/pull/') &&

‎.github/workflows/rename_package.yml‎

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name: Rename package recipe
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on:
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issue_comment:
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types: [created]
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jobs:
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rename_package:
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runs-on: ubuntu-latest
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# Only run if comment is on a PR and if it contains the magic keywords
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# Ensure the comment starts with "@delphis-bot rename" and is made by TCLamnidis
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if: >
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contains(github.event.comment.html_url, '/pull/') &&
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startsWith(github.event.comment.body, '@delphis-bot rename') &&
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github.event.repository.full_name == 'poseidon-framework/minotaur-recipes' &&
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github.event.comment.user.login == 'TCLamnidis'
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steps:
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# indication that the process has started
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- name: React on comment
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uses: peter-evans/create-or-update-comment@v2
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with:
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comment-id: ${{ github.event.comment.id }}
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reactions: rocket
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token: ${{ secrets.delphis_bot_org_token }}
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# Use the @delphis-bot token to check out so we can push later
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- uses: actions/checkout@v4
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with:
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token: ${{ secrets.delphis_bot_org_token }}
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# Action runs on the issue comment, so we don't get the PR by default
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# Use the gh cli to check out the PR
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- name: Checkout Pull Request
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run: gh pr checkout ${{ github.event.issue.number }}
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env:
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GITHUB_TOKEN: ${{ secrets.delphis_bot_org_token }}
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- name: Get package name from comment
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id: get_package_name
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run: |
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if [[ "${{ github.event.comment.body }}" =~ @delphis-bot\ rename\ ([a-zA-Z0-9_-]+)\ ([a-zA-Z0-9_-]+) ]]; then
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echo "target_package_name=${BASH_REMATCH[1]}" >> $GITHUB_OUTPUT
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echo "destination_package_name=${BASH_REMATCH[2]}" >> $GITHUB_OUTPUT
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else
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echo "No package names found in comment."
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exit 1
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fi
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- name: Check if target package exists
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id: target_check
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run: |
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target_exists='true'
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if [ ! -d "./packages/${{ steps.get_package_name.outputs.target_package_name }}" ]; then
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echo "Target package does not exist."
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target_exists='false'
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fi
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echo "target_exists=${target_exists}" >> $GITHUB_OUTPUT
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- name: Check if destination package exists
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id: destination_check
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run: |
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destination_free='true'
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if [ -d "./packages/${{ steps.get_package_name.outputs.destination_package_name }}" ]; then
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echo "Destination package already exists."
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destination_free='false'
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fi
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echo "destination_free=${destination_free}" >> $GITHUB_OUTPUT
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## DEBUG
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# - name: Post debug comment
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# uses: peter-evans/create-or-update-comment@v2
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# with:
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# issue-number: ${{ github.event.issue.number }}
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# token: ${{ secrets.delphis_bot_org_token }}
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# body: |
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# Debugging information:
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# - Target package name: `${{ steps.get_package_name.outputs.target_package_name }}`
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# - Destination package name: `${{ steps.get_package_name.outputs.destination_package_name }}`
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# - Target package exists: `${{ steps.target_check.outputs.target_exists }}`
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# - Destination package exists: `${{ steps.destination_check.outputs.destination_free }}`
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- name: Post error comment
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if: steps.target_check.outputs.target_exists == 'false' || steps.destination_check.outputs.destination_free == 'false'
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uses: peter-evans/create-or-update-comment@v2
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with:
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issue-number: ${{ github.event.issue.number }}
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token: ${{ secrets.delphis_bot_org_token }}
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body: |
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Error: Cannot rename package.
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This can be caused by one of the following reasons:
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- Target package `${{ steps.get_package_name.outputs.target_package_name }}` does not exist.
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- Destination package `${{ steps.get_package_name.outputs.destination_package_name }}` already exists.
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- name: Rename package directory
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if: >
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steps.get_package_name.outputs.target_package_name != steps.get_package_name.outputs.destination_package_name &&
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steps.target_check.outputs.target_exists == 'true' &&
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steps.destination_check.outputs.destination_free == 'true'
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id: rename_package
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run: |
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mv "./packages/${{ steps.get_package_name.outputs.target_package_name }}" "./packages/${{ steps.get_package_name.outputs.destination_package_name }}"
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for file in ./packages/${{ steps.get_package_name.outputs.destination_package_name }}/${{ steps.get_package_name.outputs.target_package_name }}*; do
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mv "${file}" "${file/${{ steps.get_package_name.outputs.target_package_name }}/${{ steps.get_package_name.outputs.destination_package_name }}}"
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done
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- name: Commit & push changes
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id: commit_changes
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if: steps.rename_package.outcome == 'success'
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run: |
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git config user.email "delphis-bot@poseidon-adna.org"
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git config user.name "delphis-bot"
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git config push.default upstream
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git add .
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git status
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git commit -m "[automated] Rename recipe from ${{ steps.get_package_name.outputs.target_package_name }} to ${{ steps.get_package_name.outputs.destination_package_name }}"
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git push

‎assets/template.config‎

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// Keep track of config versions
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minotaur_release='0.5.0' // The release tag of the poseidon-eager repository used for processing and config file retrieval
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config_template_version='0.5.0'
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package_config_version='0.5.0'
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minotaur_release='1.0.0' // The release tag of the poseidon-eager repository used for processing and config file retrieval
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config_template_version='1.0.0'
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package_config_version='1.0.0'
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minotaur_config_base="https://raw.githubusercontent.com/poseidon-framework/poseidon-eager/${minotaur_release}/conf"
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// This configuration file is designed to be a used with the nf-core/eager pipeline.
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// single file.
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// Load configuration profiles. They are loaded from the minotaur_config_base URL, main branch.
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includeConfig "${minotaur_config_base}/EVA_cluster.config" // Cluster-specific configurations for nf-core/eager execution at MPI-EVA
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// The loaded config includes code that loads the institutional configs from https://github.com/poseidon-framework/minotaur-institutional-configs.
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includeConfig "${minotaur_config_base}/Minotaur.config" // Default nf-core/eager parameters for Minotaur processing.
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// The following config file specifies BED files for on-target endogenous DNA calculation and mean coverage as well as pseudohaploid genotyping.

‎packages/2021_PattersonNature/2021_PattersonNature.config‎

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// Keep track of config versions
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minotaur_release='0.3.0dev' // The release tag of the poseidon-eager repository used for processing and config file retrieval
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config_template_version='0.3.0dev'
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package_config_version='0.3.0dev'
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minotaur_release='0.5.0' // The release tag of the poseidon-eager repository used for processing and config file retrieval
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config_template_version='0.5.0'
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package_config_version='0.5.0'
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minotaur_config_base="https://raw.githubusercontent.com/poseidon-framework/poseidon-eager/${minotaur_release}/conf"
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// This configuration file is designed to be a used with the nf-core/eager pipeline.
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Any parameters not specified in any of the config files default to their nf-core/eager default values.
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For information on all available parameters and their default values see:
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https://nf-co.re/eager/2.4.6/parameters
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https://nf-co.re/eager/2.5.1/parameters
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You can see the default values for parameters within poseidon-eager at:
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You can see the latest default values for parameters within poseidon-eager at:
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https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/Minotaur.config
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*/
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}

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