cytomining / cytomining/profiling-recipe
Migrate from subprocess to workflow language
- Dominant language
- Python
- Stars
- 11
- Forks
- 34
- PR merge metrics
- No merged PRs in 30d
Description
Explore moving from a subprocess-based pipeline step execution strategy to a workflow language.
Some examples include:
* wdl - https://github.com/openwdl/wdl
* snakemake - https://snakemake.github.io/
How we will make this decision:
* We will outline our needs for the immediate and future pipeline (some needs discussed in #11 )
* We will determine which option best serves our needs and is most compatible with our tech stack
* We will carve out sufficient, dedicated time to make an informed decision
Contributor guide
No contributing guide indexed for this repository
Research direction
Start by reviewing the pipeline needs discussed in issue #11 and the current subprocess-based execution strategy. Compare WDL and Snakemake against the immediate and future requirements and the existing Python stack. Done means documenting an informed choice and defining the migration work, but no implementation entry point is named here.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-engineering
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100