Split AlphaFold2 MSA search operations in to separate nextflow processes
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Description
Description of feature
The AlphaFold2 MSA is composed of several independent search operations which are combined as input to the model. These are run sequentially and can bottleneck predictions.
Since we already maintain a fork for generating the AlphaFold2 input data, it would be nice to split each independent search operation in to a separate process to improve parallelisation, resource allocation, recovery from failure etc. It would also be nice to take advantage of existing nf-core modules (eg hmmer_jackhmmer) which wrap the tools already used for search internally.
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 tracing the existing sequential AlphaFold2 MSA search operations in the proteinfold workflow and reviewing the maintained input-data fork and nf-core hmmer_jackhmmer module. Confirm how each independent search can become a separate Nextflow process, then verify parallel execution, resource allocation, failure recovery, and preserved AlphaFold2 input generation.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100