Transfer functional parts over

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: "Join the poseidon Slack space"
+    url: https://poseidon-8el7276.slack.com/
+    about: Discussions about everything Poseidon-Framework.

.github/ISSUE_TEMPLATE/request_a_package.md

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+---
+name: "Please add: [PACKAGE_NAME]"
+about: Request to add data from a publication to the Poseidon Package Directory
+labels: "new package"
+---
+
+<!--
+# poseidon-framework/minotaur-recipes package request
+
+Hello there!
+
+Thanks for suggesting a new publication to add to the Poseidon Package Directory!
+Please ensure you are completing all the TODOs outlined in these comments for each section.
+-->
+
+## Check for existing package
+
+I have checked the following places for the requested package and could not find
+it:
+
+- [ ] Poseidon Package Directory
+- [ ] The `packages/` directory in this repository
+- [ ] Open issues in this repository
+- [ ] Open pull requests in this repository
+
+<!--
+TODO: Please confirm that you checked the resources listed above to ensure that the requested package does not already exist under a different name than you expected.
+-->
+
+## Required information for the package
+
+- DOI of publication: https://doi.org/10.1038/s41467-018-07483-5 <- Please
+  replace this example DOI with the one for the relevant publication
+- Project accession number:
+  [PRJEB29360](https://www.ebi.ac.uk/ena/data/view/PRJEB29360) <- Please replace
+  this example ENA project link with the one for the relevant publication
+
+<!--
+TODO: Please replace the DOI and the study accession (and URL to the public sequencing data repository) above with the relevant information for the requested package
+-->
+
+## Will you work on this?
+
+If you are planning to work on comppiling the `.ssf` file required to add this
+package, please assign yourself to this issue. This helps the community
+collaborate effectively and avoid duplicating work.
+
+<!--
+We really appreciate users compiling the SSF file for packages they want added to the Poseidon Package Directory.
+If you would like to contribute but are unsure how, feel free to ask the community for help/advice at: https://poseidon-8el7276.slack.com
+-->

.github/ISSUE_TEMPLATE/update_a_package.md

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+---
+name: "Please update: [PACKAGE_NAME]"
+about: Suggest an update to an already-existing poseidon package.
+labels: "package update"
+---
+
+<!--
+# poseidon-framework/minotaur-recipes package request
+
+Hello there!
+
+Thank you for suggesting changes to a package in the Poseidon Package Directory!
+Please ensure you are completing all the TODOs outlined in these comments for each section.
+-->
+
+## Which package needs changes?
+
+Package name: `2018_Lamnidis_Fennoscandia` <- Replace the package name here with
+the name of the relevant package.
+
+<!-- TODO: Please Specify the name of the package you think needs updating -->
+
+## Check for upcoming changes
+
+I confirm there are no changes already suggested for this package that address
+my issue in:
+
+- [ ] [Open Pull Requests](https://github.com/poseidon-framework/minotaur-recipes/pulls)
+- [ ] [Open Issues](https://github.com/poseidon-framework/minotaur-recipes/issues)
+
+<!--
+TODO: Please confirm you have looked for open issues and/or pull requests suggesting changes to this package and found none.
+If an open issue or pull request exists already, and it might be addressing your issue, then consider mentioning your problem there instead of creating a new issue.
+-->
+
+## What needs changing, and why?
+
+<!--
+TODO: Please describe what you would like to see changed in the poseidon package.
+Are there some data/individuals missing? Do you disagree with the nf-core/parameters used? The more information you provide here, the better.
+-->
+
+## (optional) What are the changes you'd like?
+
+<!--
+TODO: If you have a specific parameter that you would like to see changed, please list it here. Otherwise you can leave this section empty.
+-->
+
+## (optional) How did you realise something needs updating?
+
+<!--
+TODO: If you came across an error with the Poseidon package resulting from this processing while running some analysis, please give information that might help us reproduce the problems here.
+If this section is not relevant, you can leave it empty.
+-->

.github/PULL_REQUEST_TEMPLATE.md

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+<!--
+# poseidon-framework/minotaur-recipes package request
+
+Hello there!
+
+Thanks for suggesting a new publication to add to the Poseidon Package Directory!
+Please ensure you are completing all the TODOs outlined in these comments for each section.
+-->
+
+Closes #XXX <!-- TODO: Please link the issue requesting the package here. -->
+
+## PR Checklist
+
+- [ ] Add the appropriate label to your PR (`new package` or `package_update`).
+- [ ] The PR title is in the format `Add/update package: {package_name}`.
+- [ ] The PR description includes a link to the issue requesting the package its update. (Add to `Closes #XXX` above.)
+
+If adding a package:
+
+- [ ] This PR contains a sequencingSourceFile (`.ssf`) for the requested package.
+- [ ] The name of the `.ssf` file(s) matches the package name (i.e. `packages/2023_my_package/2023_my_package.ssf`).
+- [ ] Comment `@delphis-bot create backbone` to this pull request to awaken Poseidon's trusty helper. (This should be repeated whenever changes are made to the SSF file contents).
+
+Delphis-bot will then add a number of files to the PR. Check that they are all there:
+
+- [ ] The file `packages/{package_name}/{package_name}.tsv` was added to the PR.
+- [ ] The file `packages/{package_name}/{package_name}.tsv_patch.sh` was added to the PR from template.
+- [ ] The file `packages/{package_name}/script_versions.txt` was added to the PR.
+- [ ] The file `packages/{package_name}/{package_name}.config` was added to the PR from template.
+<!-- TODO: Follow the steps outlined above and tick them off as you go. -->
+
+## Human validation
+
+<!-- TODO: Please do the minimal validation of the files outlined below -->
+
+### Package SSF file (`*.ssf`)
+
+- [ ] I confirm that the `poseidon_IDs`, `udg`, and `library_built` are filled and correct.
+- [ ] I made sure to leave `notes` where necessary to explain any special cases/judgement calls made for data entries.
+
+### Package TSV file (`*.tsv`)
+
+- [ ] I confirm that the `UDG`, `Strandedness` columns are correct for each library.
+- [ ] I confirm that the `R1_target_file` and `R2_target_file` columns point to the correct FastQ files for the library (i.e. consistent with SSF file).
+
+### Package config file (`*.config`)
+
+The template config file includes a few `TODO` statements, and information about them. Please ensure that you:
+
+- [ ] I have selected the appropriate config for the CaptureType of the package.
+- [ ] If any nf-core/eager parameters need to be altered from their defaults, I have added them within the `params` section at the end of the package config file.

.github/workflows/PR_checks.yml

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+name: CI for  PRs that add or update packages
+# This workflow runs minimal required validation steps for merging of PRs that add or update packages
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  ssf_validation:
+    name: Validate SSF
+    ## Run on PRs that contain the right label
+    if: contains(github.event.pull_request.labels.*.name, 'new package') || contains(github.event.pull_request.labels.*.name, 'package update')
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      ## Commands that require a github token cannot be used here, because forked repos do not have access to secrets.
+      ## Use the gh cli to check out the PR
+      # - name: Checkout Pull Request
+      #   run: gh pr checkout ${{ github.event.pull_request.number }}
+      #   env:
+      #     GITHUB_TOKEN: ${{ secrets.delphis_bot_auth_token }}
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.10.11
+
+      - name: Get changed files
+        id: changes
+        # Set outputs using the command.
+        run: |
+          echo "PR base sha: ${{ github.event.pull_request.base.sha }}"
+          echo "PR head sha: ${{ github.sha }}"
+          echo "ssf=$(git diff --name-only --diff-filter=ACMRT ${{ github.event.pull_request.base.sha }} ${{ github.sha }} | grep '.ssf$')" >> $GITHUB_OUTPUT
+
+      - name: Check SSF
+        if: ${{ steps.changes.outputs.ssf }}
+        run: |
+          ## Validate contents of each SSF file.
+          for ssf_fn in ${{ steps.changes.outputs.ssf }}; do
+            echo "Validating: '${ssf_fn}'"
+            python scripts/ssf_validator.py ${ssf_fn}
+          done

.github/workflows/create_package_skeleton.yml

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+name: Create additional PR files
+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 backbone') &&
+      github.repository == 'poseidon-framework/poseidon-eager'
+    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_auth_token }}
+
+      # Use the @delphis-bot token to check out so we can push later
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.delphis_bot_auth_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: ${{ secrets.delphis_bot_auth_token }}
+
+      - uses: actions/setup-node@v3
+
+      - name: Get package names from added ssf files
+        id: get_package_names
+        run: |
+          offending_ssfs=''
+          package_names=''
+
+          while read r; do
+            package_name="$(basename -s .ssf ${r})"
+            package_dir="$(basename $(dirname ${r}))"
+            if [[ ${package_name} != ${package_dir} ]]; then
+              offending_ssfs+="${r} "
+            fi
+            package_names+="${package_name} "
+          done < <( gh api /repos/poseidon-framework/poseidon-eager/pulls/${{ 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_auth_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_auth_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/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 processing backbone 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

.prettierrc

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+{
+  "printWidth": 80,
+  "tabWidth": 2,
+  "useTabs": false,
+  "max-line-length": [true, { "limit": 120 }],
+  "proseWrap": "always"
+}