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MDU-PHL
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bohra
A pipeline for bioinformatics analysis of bacterial genomes
GNU General Public License v3.0
13
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3
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Using -c doesnt_exist.tab should fail
#83
tseemann
opened
4 days ago
0
Support for NTC and PTC samples
#82
tseemann
opened
1 month ago
0
Update kraken2
#81
kristyhoran
closed
4 weeks ago
1
Useful enhancements
#80
JA-Lacey
opened
1 month ago
0
Emmtyper
#79
JA-Lacey
opened
1 month ago
0
An error when --kraken_db provides available kraken database path
#78
abcdtree
opened
4 months ago
0
Limit the size of the tree viewer to the size of the window
#77
ckhiggs
opened
6 months ago
0
Int bug if sample name is an interger
#76
kristyhoran
opened
9 months ago
0
Fix up core genome graph
#75
kristyhoran
opened
9 months ago
0
Software used for the specific analysis
#74
ckhiggs
opened
9 months ago
0
Addition of reference genome name and details to report
#73
ckhiggs
opened
9 months ago
0
Containerized Bohra installation
#72
tetedange13
opened
1 year ago
1
"altair" Python package missing from bohra conda recipe ?
#71
tetedange13
opened
1 year ago
0
There is something wrong with your reference file. Valid file types are .fasta, .gbk, .fasta.gz, .gbk.gz. Please check your inputs and try again.
#70
Vikash84
opened
1 year ago
2
Add tests
#69
kristyhoran
closed
8 months ago
0
Annotation module for 'bakta'
#68
tseemann
opened
1 year ago
1
Add DOI and PMID for all tools used
#67
tseemann
opened
1 year ago
0
Clarify babykraken is not actually "useful"
#66
tseemann
opened
1 year ago
0
Add typers and tests
#65
kristyhoran
closed
1 year ago
2
Make tests suite
#64
kristyhoran
closed
1 year ago
2
Add install script
#63
kristyhoran
closed
1 year ago
1
Which is the real Bohra repo?
#62
tseemann
closed
1 year ago
0
Bohra fails with no params
#61
tseemann
closed
1 year ago
0
Remove alert from iqtree
#60
kristyhoran
closed
1 year ago
0
Thread pool reached error
#59
kristyhoran
closed
1 year ago
1
Too many columns for mlst when duplicate alleles are foun
#58
kristyhoran
closed
1 year ago
0
Substitute panaroo for roary
#57
kristyhoran
closed
2 years ago
0
Partition out tasks
#56
kristyhoran
closed
1 year ago
0
Check mlst
#55
kristyhoran
closed
2 years ago
0
Tidy up directory
#54
kristyhoran
closed
1 year ago
0
Investigate regex for reads
#53
kristyhoran
closed
2 years ago
0
Update CLI and config with snippy params
#52
kristyhoran
closed
2 years ago
0
Keep amrfinder output
#51
kristyhoran
closed
2 years ago
0
Process customisation
#50
kristyhoran
closed
1 year ago
0
Nextflow - conversion tested
#49
kristyhoran
closed
2 years ago
0
fail gracefully if files are not accessible
#48
kristyhoran
closed
3 years ago
3
Add versions to software check
#47
kristyhoran
closed
2 years ago
0
-mdu option does not prefill kraken or maybe others
#46
abcdtree
closed
3 years ago
1
Small miss used variable in bohra
#45
abcdtree
closed
2 years ago
1
Set --threads to kraken2 (and check other tools).
#44
andersgs
closed
3 years ago
1
Rerunning preview after running snps fails
#43
kristyhoran
closed
3 years ago
0
report writing fails when report.toml too large
#42
kristyhoran
closed
3 years ago
0
rerun bug
#41
kristyhoran
closed
3 years ago
1
MLST bug
#40
kristyhoran
closed
3 years ago
0
Bug when reference is FASTA
#39
andersgs
closed
4 years ago
1
Include ref(s) in preview mode
#38
andersgs
closed
4 years ago
1
Add 'check' subcommand
#37
tseemann
closed
4 years ago
0
nulla2bohra requirements
#36
tseemann
closed
4 years ago
0
"bohra run" no params is a traceback mess
#35
tseemann
closed
4 years ago
0
pandas "ix" deprecated
#34
willpitchers
closed
4 years ago
0
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