Dev

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,43 +1,25 @@
-<!--
-# poseidon-framework/poseidon-eager 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.
+<!-- Still preliminary. -->
+
+When a new release is made for minotaur, the following steps should be taken:
+
+- Update the CHANGELOG.md to include a description of all changes.
+- Add Release date and bump version number to CHANGELOG.md
+- If the eager version was changed:
+  - [ ] Update the eager version in the [minotaur-recipes repo config temp](https://github.com/poseidon-framework/minotaur-recipes/blob/main/assets/template.config)
+  - [ ] Update [Minotaur's MultiQC configuration file](https://github.com/poseidon-framework/poseidon-eager/blob/main/conf/minotaur_multiqc_config.yaml)
+    - [ ] Pull the latest MultiQC config from [nf-core/eager](https://github.com/nf-core/eager/blob/master/assets/multiqc_config.yaml)
+    - [ ] Apply the required Minotaur tweaks to the config file.
+    - [ ] Update the eager version in `scripts/populate_janno.py`
+- Update the version number in the following files:
+  - [ ] scripts/download_and_localise_package_files.sh
+  - [ ] scripts/create_eager_input.sh
+  - [ ] scripts/minotaur_packager.sh
+  - [ ] scripts/validate_downloaded_data.sh
+  - [ ] scripts/run_eager.sh
+  - [ ] scripts/populate_janno.py
+  - [ ] scripts/download_ena_data.py
+- Create new release, release tag, and name.
+
+After the release:
+
+- Update the poseidon-eager release tag used in the [minotaur-recipes repo](https://github.com/poseidon-framework/minotaur-recipes/blob/main/assets/template.config).

.gitignore

@@ -8,3 +8,4 @@ testing_assets/
 packages/
 poseidon_packages/
 .tmp/
+packages/