issues
search
ctmrbio
/
BACTpipe
BACTpipe: An assembly and annotation pipeline for bacterial genomics
https://bactpipe.readthedocs.org
MIT License
20
stars
7
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Prokka isn't running if Kraken fails
#173
thorellk
opened
2 years ago
0
bioconda::prokka environment error
#172
shigdon
opened
2 years ago
1
Hotfix for syncing input for prokka
#171
abhi18av
closed
3 years ago
14
Prokka process gets mixed inputs
#170
boulund
closed
3 years ago
5
Include config file for large raw files?
#169
thorellk
opened
3 years ago
11
Add Sandra in citation in docs
#168
boulund
closed
3 years ago
0
Merge master with updated citation to dev
#167
boulund
closed
3 years ago
0
Changelog 3.1
#166
emilio-r
closed
3 years ago
2
Update docker file to accomodate kraken
#165
abhi18av
closed
3 years ago
6
Invalid process definition -- Unknown keyword 'stub' @ line 20, column 5
#164
bioramg
closed
3 years ago
5
Replace sendsketch with kraken2
#163
boulund
closed
3 years ago
6
Replace SendSketch with Kraken2
#162
boulund
closed
3 years ago
2
Check signalp dependency and dockerize BACTpipe
#161
abhi18av
closed
3 years ago
0
Develop
#160
thorellk
closed
3 years ago
46
Workaround for sketch skipping
#159
emilio-r
closed
3 years ago
0
Reduce the search scope for MultiQC
#158
boulund
closed
3 years ago
2
Add ctmr_gandalf profile to available options
#157
boulund
closed
3 years ago
0
Add ctmr_gandalf profile
#156
boulund
closed
3 years ago
0
Made shovill.log standard output
#155
emilio-r
closed
3 years ago
3
Made shovill.log standard output
#154
emilio-r
closed
3 years ago
1
Rename ctmrnas profile
#153
boulund
closed
3 years ago
0
shovill.log output as standard
#152
emilio-r
closed
3 years ago
6
Add automated testing via Github workflows
#151
abhi18av
closed
3 years ago
1
Add cpus to shovill
#150
abhi18av
closed
3 years ago
3
SHOVILL process running with default threads 8
#149
boulund
closed
3 years ago
1
Warn user if signalp is missing if prokka_gram is true
#148
boulund
opened
3 years ago
9
The docs still makes references to database paths
#147
boulund
closed
3 years ago
2
Running with the latest stable nextflow version (20.10.0) does not work
#146
boulund
closed
3 years ago
2
Limit MultiQC search options
#145
thorellk
closed
3 years ago
7
Shovill-Sendsketch skipping
#144
emilio-r
closed
3 years ago
31
Fix exit message
#143
abhi18av
closed
3 years ago
0
BACTpipe workflow completed without errors
#142
thorellk
closed
3 years ago
1
Cleanup sendsketch to prokka
#141
boulund
closed
3 years ago
15
Synchronize develop branch with master
#140
boulund
closed
3 years ago
3
Update changelog
#139
boulund
closed
3 years ago
1
The documentation for 3.0 is not automatically updated by sphinx
#138
thorellk
closed
3 years ago
4
Update citation/publish pipeline
#137
thorellk
opened
3 years ago
25
Update flowchart for new 3.0 options
#136
emilio-r
closed
3 years ago
0
Add process stubs and update the files to be published
#135
abhi18av
closed
3 years ago
6
Version-3.0 release
#134
abhi18av
closed
3 years ago
16
Improve error handling and user experience in the python scripts.
#133
abhi18av
closed
3 years ago
1
Decide on what files to output
#132
thorellk
closed
3 years ago
23
Remove stdout from SCREEN_FOR_CONTAMINANTS process
#131
abhi18av
closed
3 years ago
1
BACTpipe v3.0
#130
abhi18av
closed
3 years ago
0
Integrate renaming script pre sendsketch
#129
thorellk
closed
3 years ago
13
emilio branch sendsketch_to_prokka.py gives incorrect output
#128
thorellk
closed
3 years ago
50
Adapt prokka as per the bacterial profile
#127
abhi18av
closed
3 years ago
9
Make the pipeline tower friendly and update docs with the instructions
#126
abhi18av
opened
3 years ago
0
Joint Zoom meeting to discuss next steps?
#125
thorellk
closed
3 years ago
5
Feat: Modularize the code and remove dangling channels and outputs
#124
abhi18av
closed
3 years ago
6
Next