Consider passing the annotation tool output to modules input for more standardization
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Description
Description of feature
Currently, some modules take in .fna as an input rather than taking in .faa as an input from the annotation tool assigned. This might create diffrerences in the way prediction modules particular covering teh BGC and ARG workflows, because each module runs a different annotation tool. To standardise this more, i would suggest to consider checking the 'BGC and ARG' modules to ensure, if possible, that they take already annotated '.faa' files from the annotation tool.
- MACREL
- GECCO
- DEEPBGC
- all ARG tools
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Research direction
Start by reviewing the BGC modules MACREL, GECCO, and DEEPBGC, followed by all listed ARG tools, to trace whether they consume .fna files or annotated .faa output. Compare how each module receives annotation-tool results and identify the workflow checks needed. Done means the applicable modules consistently use the assigned annotation tool's annotated .faa output.
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
- 38/100