cfe-lab / cfe-lab/MiCall

Marking results folders

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enhancement
Dominant language
Python
Stars
21
Forks
11
Avg merge
12h 5m
Merged PRs (30d)
24

Description

During the release of version 6.3, I had some ideas for how to make the results easier to work with.

  • Put the version of the pipeline in the doneprocessing file, so we can reliably identify which version the results came from, even if someone moves the folder.
  • Maybe we should mark the version as failed instead of the entire run. That way you could try again with the next release of the pipeline. If a run breaks on the new version of the pipeline, you can still go back and look at the results from the old version. Maybe we need both, so you could tell the monitor to stop trying with a really bad run. This is a separate issue: #101.
  • Make the Micall page display a warning with the results if it finds a results folder without the doneprocessing file. That way you can trigger a rerun by removing the doneprocessing or errorprocessing file without worrying about leaving an incomplete result set or having to clean out the entire result set. (That makes me nervous.)

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by locating the code that creates or checks the doneprocessing and errorprocessing files, then trace the Micall page's handling of results folders. The issue's stated outcomes are to record the pipeline version, distinguish incomplete folders, and display a warning when doneprocessing is absent; version-failure handling is tracked separately in #101.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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