Allow submitters to set the snpSet of that gets propagated to the POSEIDON.yml of the package #12
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| name: Create package recipe from SSF | |
| on: | |
| issue_comment: | |
| types: [created] | |
| jobs: | |
| deploy: | |
| # Only run if comment is on a PR with the main repo, and if it contains the magic keywords | |
| if: > | |
| contains(github.event.comment.html_url, '/pull/') && | |
| startsWith(github.event.comment.body, '@delphis-bot create recipe') && | |
| github.repository == 'poseidon-framework/minotaur-recipes' | |
| runs-on: ubuntu-latest | |
| steps: | |
| # indication that the process has started | |
| - name: React on comment | |
| uses: peter-evans/create-or-update-comment@v2 | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: eyes | |
| token: ${{ secrets.delphis_bot_org_token }} | |
| # Use the @delphis-bot token to check out so we can push later | |
| - uses: actions/checkout@v3 | |
| with: | |
| token: ${{ secrets.delphis_bot_org_token }} | |
| # Action runs on the issue comment, so we don't get the PR by default | |
| # Use the gh cli to check out the PR | |
| - name: Checkout Pull Request | |
| run: gh pr checkout ${{ github.event.issue.number }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.delphis_bot_org_token }} | |
| - uses: actions/setup-node@v3 | |
| - name: Get package names from added ssf files | |
| id: get_package_names | |
| run: | | |
| offending_ssfs='' | |
| package_names='' | |
| while read r; do | |
| package_name="$(basename -s .ssf ${r})" | |
| package_dir="$(basename $(dirname ${r}))" | |
| if [[ ${package_name} != ${package_dir} ]]; then | |
| offending_ssfs+="${r} " | |
| fi | |
| package_names+="${package_name} " | |
| done < <( gh api /repos/poseidon-framework/minotaur-recipes/pulls/${{ github.event.issue.number }}/files -q '.[].filename' | grep '.ssf$' ) | |
| echo "offending_ssfs=${offending_ssfs% }" >>$GITHUB_OUTPUT | |
| echo "package_names=${package_names% }" >>$GITHUB_OUTPUT | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.delphis_bot_org_token }} | |
| - name: Post comment listing offending packages | |
| if: steps.get_package_names.outputs.offending_ssfs != '' | |
| uses: peter-evans/create-or-update-comment@v2 | |
| with: | |
| issue-number: ${{ github.event.issue.number }} | |
| token: ${{ secrets.delphis_bot_org_token }} | |
| body: | | |
| SSF files MUST be named after their respective package. The following SSF files break this rule: | |
| ${{ steps.get_package_names.outputs.offending_ssfs }} | |
| - name: Create eager TSV from SSF | |
| id: create_tsv | |
| if: steps.get_package_names.outputs.offending_ssfs == '' | |
| run: | | |
| for package_name in ${{ steps.get_package_names.outputs.package_names }}; do | |
| ./scripts/delphis-bot_scripts/create_eager_input.sh ${package_name} | |
| done | |
| - name: Add nextflow config from template | |
| id: add_config | |
| if: steps.get_package_names.outputs.offending_ssfs == '' | |
| run: | | |
| for package_name in ${{ steps.get_package_names.outputs.package_names }}; do | |
| cp ./assets/template.config ./packages/${package_name}/${package_name}.config | |
| done | |
| - name: Add tsv_patch from template | |
| id: add_tsv_patch | |
| if: steps.get_package_names.outputs.offending_ssfs == '' | |
| run: | | |
| for package_name in ${{ steps.get_package_names.outputs.package_names }}; do | |
| cp ./assets/template.tsv_patch.sh ./packages/${package_name}/${package_name}.tsv_patch.sh | |
| chmod +x ./packages/${package_name}/${package_name}.tsv_patch.sh | |
| done | |
| - name: Commit & push changes | |
| id: commit_changes | |
| if: steps.create_tsv.outcome == 'success' | |
| run: | | |
| git config user.email "[email protected]" | |
| git config user.name "delphis-bot" | |
| git config push.default upstream | |
| git add . | |
| git status | |
| git commit -m "[automated] Create package recipe from SSF files" | |
| git push | |
| # # indication that the process is done | |
| # - name: React on comment | |
| # if: steps.commit_changes.outcome == 'success' || steps.commit_changes.outcome == 'failure' | |
| # uses: peter-evans/create-or-update-comment@v2 | |
| # with: | |
| # comment-id: ${{ github.event.comment.id }} | |
| # reactions: eyes |