Consider using `collectFile` to optimise aggregating of results of bin statistics steps
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Description
Description of feature
As described by @maxibor here: https://github.com/nf-core/mag/pull/489#issuecomment-1791336502
Where originally we were getting file name clashes of bins sent to (microbes) and skipped (eukaryotes) around DASTool. This was fixed by Maxime by adding correct prefixes with all the information, but it may make sense to use collectFile to merge the contents which would avoid such clashes. However there were some things to explore as described in the PR above.
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 discussion in nf-core/mag pull request 489, especially the linked issue comment, to understand the file-clash history and the unexplored concerns around collectFile. Done means deciding whether collectFile can safely aggregate the bin-statistics results without reintroducing clashes, then documenting or implementing that decision in the workflow.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100