MDU-PHL bohra issues - Githubissues

MDU-PHL / bohra

A pipeline for bioinformatics analysis of bacterial genomes

GNU General Public License v3.0

19 stars 4 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

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
run/rerun `-f` flag not working

#33 willpitchers closed 4 years ago
1
--dryrun should be --dry-run and -n

#32 tseemann closed 5 years ago
0
add in a setup command

#31 kristyhoran closed 5 years ago
0
error in dryrun

#30 kristyhoran closed 5 years ago
0
error in unzip

#29 kristyhoran closed 5 years ago
0
cluster.json and snakemake command

#28 kristyhoran closed 5 years ago
0
Add support for contig in core genome graph

#27 kristyhoran closed 5 years ago
0
What is --workdir ?

#26 tseemann closed 5 years ago
1
Typo in my name

#25 tseemann closed 5 years ago
0
Badge says python 3.6 but it all seems to be 3.7

#24 tseemann closed 5 years ago
0
NameError: name 'parser' is not defined

#23 tseemann closed 5 years ago
2
Add annotations to the phylo tree

#22 tseemann opened 5 years ago
0
Phylo tree missing a scale

#21 tseemann closed 4 years ago
2
Round "Depth" to an integer

#20 tseemann closed 5 years ago
0
Etiology - did you mean Etymology?

#19 tseemann closed 5 years ago
0
Add setup instructions for all databases

#18 tseemann closed 1 year ago
0
add zoom to tree

#17 kristyhoran closed 4 years ago
1
Add in end-to-end test for circleci

#16 kristyhoran closed 1 year ago
1
add example reports

#15 kristyhoran opened 5 years ago
0
conda and brew

#14 kristyhoran closed 5 years ago
0
Update README.md for installation options

#13 kristyhoran closed 5 years ago
0
pip installation

#12 kristyhoran closed 5 years ago
0
singularity support

#11 kristyhoran closed 1 year ago
0
seqtk vs fq

#10 kristyhoran closed 5 years ago
1
Use `shutil.which` instead of `subprocess.run` to find out executables

#9 andersgs closed 5 years ago
0
Best practice for `logging`

#8 andersgs closed 5 years ago
1
Parse out argument processing into a new function

#7 andersgs closed 5 years ago
1
Add docstring to top `bohra.py` and `__init__.py`

#6 andersgs closed 5 years ago
4
Move `test` to top directory

#5 andersgs closed 5 years ago
2
Add __version__ to __init__.py

#4 andersgs closed 5 years ago
2
Add appropriate classifiers to setup.py

#3 andersgs closed 5 years ago
1
Automate push to PyPI

#2 andersgs closed 5 years ago
2
"or Ion Torrent read sets."

#1 tseemann closed 5 years ago
0

MDU-PHL / bohra

issues

Include ref(s) in preview mode

Add 'check' subcommand

nulla2bohra requirements

"bohra run" no params is a traceback mess

pandas "ix" deprecated

run/rerun `-f` flag not working

--dryrun should be --dry-run and -n

add in a setup command

error in dryrun

error in unzip

cluster.json and snakemake command

Add support for contig in core genome graph

What is --workdir ?

Typo in my name

Badge says python 3.6 but it all seems to be 3.7

NameError: name 'parser' is not defined

Add annotations to the phylo tree

Phylo tree missing a scale

Round "Depth" to an integer

Etiology - did you mean Etymology?

Add setup instructions for all databases

add zoom to tree

Add in end-to-end test for circleci

add example reports

conda and brew

Update README.md for installation options

pip installation

singularity support

seqtk vs fq

Use `shutil.which` instead of `subprocess.run` to find out executables

Best practice for `logging`

Parse out argument processing into a new function

Add docstring to top `bohra.py` and `init.py`

Move `test` to top directory

Add version to init.py

Add appropriate classifiers to setup.py

Automate push to PyPI

"or Ion Torrent read sets."