nf-core / nf-core/denovotranscript
Consider splitting Trinity stages into separate tasks
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- Dominant language
- Nextflow
- Stars
- 26
- Forks
- 3
- PR merge metrics
- No merged PRs in 30d
Description
Description of feature
It would be great if the pipeline split each of the Trinity stages (jellyfish, inchworm, chrysalis, butterfly) into distinct processes so they could be better targeted to cpu and memory resources required for each task and make more efficient use of HPC (and Batch etc) resources.
An example implementation of this for reference would be: https://github.com/marcodelapierre/trinity-nf
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 reviewing the pipeline workflow and the referenced trinity-nf implementation. Map the jellyfish, inchworm, chrysalis, and butterfly stages, then determine how each can run as a distinct process with independently targeted CPU and memory resources. Done means all four stages are separately schedulable and the pipeline remains functional on HPC or Batch resources.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, data-engineering, hpc
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100