nf-core / nf-core/phageannotator
COBRA options schema are listed as strings when they should be ints
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Description
Description of the bug
Trying to run COBRA and it requires three params, --cobra_assembler, --cobra_mink, --cobra_maxk. Currently the mink and maxk are expected to be strings, but they should be ints.
Related, cobra_assembler can only be "idba", "metaspades", or "megahit" per its documentation.
Command used and terminal output
Relevant files
No response
System information
No response
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
No relevant files are identified in the issue. Start by locating the COBRA options schema and checking how cobra_mink, cobra_maxk, and cobra_assembler are declared, then compare those declarations with the documented parameter requirements. Done means the numeric options accept integers and the assembler option permits only the documented values, with any relevant validation passing.
Written by the indexing model from the issue text.
Assessment
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100