cfe-lab / cfe-lab/MiCall

Find results folder through run parameters

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

Description

If a MiSeq run gets delayed and run after the date in the run name, then the run folder name won't match the run name in the sample sheet and the lab_miseq_run table. The QAI Micall page uses that date to find the run folder, so it can't find the run folder.

Make the QAI Micall page look up the folder name in the miseqqc_runparameters table instead of calculating it from the run name.

As an example, the 170228_M01841_0287_000000000-AYA5T run folder used the "27-Feb-2017.M01841" run name.

###Workaround###

  1. Load the sample sheet in QAI, change the run name to match the run folder, then save it.
  2. In the database, update the miseqqc_runparameters.experimentname field to match the date in the run name.
  3. Copy the new sample sheet to the run folder.
  4. Delete the results from the run folder, then wait for the MiSeq monitor to submit it to Kive and upload the results.
  5. Delete the old run from QAI to avoid confusion, including related tables.

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 at the QAI Micall page code that locates a MiSeq run folder, then inspect the miseqqc_runparameters table and its experimentname field. Verify the delayed-run example resolves the folder 170228_M01841_0287_000000000-AYA5T from the stored run parameters rather than deriving the date from the run name.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend, databases
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
48/100

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