cfe-lab / cfe-lab/MiCall

Let users add new projects

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

Description

Richard H. asked that:

"Research" folks can add their own reference, say by linking to a fasta with a different project (and once added, that reference can exist from then on).
So that if we want to test, say, measles or Zika, we can just add them.

In order to keep the runs reproducible, we can't let users change the pipeline itself. Instead, add another input file with extra seed references and coordinate references.

  • load extra config file from project_config.py
  • pass extra config file to project_config.py from all the steps
  • let users create a new project in MiCall and link to it from the layout page
  • build extra config file in MiSeq monitor (look for project names that aren't in regular project config file)

Contributor guide

No contributing guide indexed for this repository

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 tracing project_config.py through all pipeline steps, then inspect how MiSeq monitor identifies project names and how the layout page links projects. Done means an extra config file can supply seed and coordinate references without changing the pipeline, users can create and link projects in MiCall, and unknown project names produce that file.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

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