BACTpipe
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ctmrbio
BACTpipe: An assembly and annotation pipeline for bacterial genomics
I just ran BACTpipe over ~70 samples and for some Kraken failed due to out of memory problems. Unfortunately this means prokka didn't run either. I think we should change...
Hello, I was attempting BACTpipe runs on ctmr-gandalf with a test set of 2 isolate pe-fastq samples when unexpectedly the system encountered an error during the Prokka module. The Git...
I just bumped into the issue of having excessively large raw fastq files per sample which leads to that `fastp` times out with the current allocations in the rackham config....
With the 3.0 release we should update the Zenodo citation so that the correct people are acknowledged. Should we also try to publish the pipeline as some kind of short...
I would like BACTpipe to detect if `signalp` is missing if `prokka_gram` is set to true, and warn the user that prokka requires signalp if combined with the `prokka_gram` option...
As a stretch-goal for the next main version of the workflow, I'd like us to implement automated regression testing. It's not very difficult, and will improve our ability to catch...
To gather assembly stats.
To add the possibility of performing hybrid assemblies of Nanopore/PacBio and Illumina data using `hybridSPAdes` would be nice. Need to think through how much of data preprocessing that needs to...
We should consider adding a CONTRIBUTING (plain text file) in the root of the repo that will contain contributing guidelines for BACTpipe. We should include a small checklist for important...