Add package: 2023_Rodriguez_Varela

[Helsinki-Ronan]

Linked to #36

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 or updating 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 recipe 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.

Human validation

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.

[Helsinki-Ronan]

@delphis-bot create recipe

[TCLamnidis]

Hey @Helsinki-Ronan! Thanks for submitting a recipe. I see this is still a draft PR, so I will not look into specifics, but I had a comment regarding the process.

Closes no issue as this is a new package request

You should create an issue to request the package before opening a PR to add the recipe. The issue is then used to track the progress of the processing and is closed (by us) only once the recipe output has been integrated into the minotaur-archive. 🙂

See https://www.poseidon-adna.org/#/minotaur?id=what-is-the-processing-status-of-the-package-i-requested

Once the recipe is ready, please mark it as "Ready for review" and I will take a look. 😁

[TCLamnidis]

@Helsinki-Ronan There appear to be multiple formatting errors in the SSF file.
See here for the details.
Please update the SSF file until it passes validation, and then retrigger Delphis-bot to recreate the recipe, so the correctly formatted information gets propagated to the auxilliary recipe files.

[stschiff]

Any update, @Helsinki-Ronan? Do you need help with this?

[Helsinki-Ronan]

@delphis-bot create recipe

[Helsinki-Ronan]

Review needed

[TCLamnidis]

@delphis-bot create recipe
To update package config to latest version.