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Hello,
This worked for me (python 3 code):
`qc_file = Path(output.MDU_QC).open('w')
qc_file.write(f'ISOLATE,SPECIES_EXP,SPECIES_OBS,TEST_QC\n{params.running_dir},Salmonella e…
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Hi Kristy,
In the old version (https://github.com/MDU-PHL/Coreugate), the input file could be reads or assemblies. However, according to my understanding, in this new version, the input file could on…
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Hi,
First, thanks for developping `bohra` !
### Context
Version of `bohra` : 2.3.2
I installed `bohra` through `conda` and ran `bohra init`
But then running `bohra run --pipeline preview`…
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It would be useful to have the modules in separate files, you can then build a catalogue of modules (perhaps in its own repo) that you can use across workflows and pipelines.
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This causes the `stype_cli.py parse` to fail when parsing MDU IDs.
One approach would be to add a dummy MDU ID (say 9999-9999) and separate each positive control with an item code. That way, it sho…
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Hi Jason,
I think @tseemann has changed some wording in the Makefile. So, the line in nullarbor-spades-fast.py `if not re.search('This file is automatically generated by the Nullarbor software', …
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When using the 'all' filter option I get the following error:
PS C:\Users\Lennert\workspaces\who2tbp> who2tbp --filter all WHO-UCN-GTB-PCI-2021.7-eng.xlsx > tbdb_who.py
[who2tbp.exe – 2021-07-16 0…
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(bohra) [vsingh@vdl]$ bohra run -p full -i isolates.tab -r ./NC_012925.1.fasta.gz
[INFO:06/21/2023 11:52:12 AM] Bohra is being run in /home/vsingh/vdl/Ssuis/ by vsingh on 2023-06-21.
[INFO:06/21/…
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