test on a real dataset
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Description
I tested pipeline on Kremer dataset ( ~119 samples). The goals are:
- check size of
savedObjectsandcachedirectories in fraser - get some resource usage reports for optimize resource setting of each process
- get some rough comparison with old pipeline
later it might also interesting to know Storage footprint
- Intermediate (scratch) vs final files
- Storage duplication
- Compute time as function of input (number of samples vs time)
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading the pipeline's existing Kremer dataset run and the linked dataset description. Reproduce the approximately 119-sample run, then review the completed resource and comparison results before measuring intermediate versus final storage, duplication, and compute time as sample count changes. Done means these measurements are recorded for the pipeline.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, data, performance
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100