Comments (2)
thorellk
commented on August 28, 2024
Do you mean the prokka reference path @boulund? This is a feature we use regularly.
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boulund
commented on August 28, 2024
I was mostly thinking of this line:
https://github.com/ctmrbio/BACTpipe/blame/master/docs/source/running.rst#L40
When running BACTpipe, you will most likely have to modify the paths for some parameters so that BACTpipe can find reference databases etc.
As far as I know, this line is a remnant from the old version that required a mash screen database path. What do you think? Just want to minimize the risk for confusion for new people reading the docs.
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Related Issues (20)
- Update flowchart for new 3.0 options
- Update citation/publish pipeline HOT 25
- The documentation for 3.0 is not automatically updated by sphinx HOT 4
- Update changelog HOT 1
- BACTpipe workflow completed without errors HOT 1
- Shovill-Sendsketch skipping HOT 31
- Limit MultiQC search options HOT 7
- Running with the latest stable nextflow version (20.10.0) does not work HOT 2
- Warn user if signalp is missing if prokka_gram is true HOT 9
- SHOVILL process running with default threads 8 HOT 1
- Add automated testing via Github workflows HOT 1
- shovill.log output as standard HOT 6
- Replace SendSketch with Kraken2 HOT 2
- Invalid process definition -- Unknown keyword 'stub' @ line 20, column 5 HOT 5
- Changelog 3.1 HOT 2
- Include config file for large raw files? HOT 11
- Prokka process gets mixed inputs HOT 5
- bioconda::prokka environment error HOT 1
- Prokka isn't running if Kraken fails
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