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rotary-genomics
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rotary
Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements
BSD 3-Clause "New" or "Revised" License
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Refactor subcommand calls in rotary repair.py
#66
LeeBergstrand
closed
10 months ago
2
Bug fixes env pathing and file extentions
#65
LeeBergstrand
closed
10 months ago
0
Bug fixes env pathing and file extentions
#64
LeeBergstrand
closed
10 months ago
2
End repair
#63
jmtsuji
closed
10 months ago
18
Location of conda env directory
#62
jmtsuji
closed
10 months ago
4
File naming error in sample.py
#61
jmtsuji
closed
10 months ago
2
Integrate repair.py into the rotary CLI
#60
jmtsuji
closed
4 months ago
1
Allow for mixture of samples with or without short-read data.
#59
LeeBergstrand
opened
10 months ago
1
Add Unified End Repair Python Script
#58
LeeBergstrand
closed
10 months ago
2
New hmm download
#57
LeeBergstrand
closed
10 months ago
2
Develop
#56
LeeBergstrand
closed
10 months ago
0
add code to download tigrfam hmms
#55
LeeBergstrand
closed
10 months ago
0
End repair
#54
LeeBergstrand
closed
10 months ago
0
Auto-naming of samples may have collision issues.
#53
LeeBergstrand
closed
10 months ago
10
Reverse fix to temporary work around in finalize assembly rule.
#52
LeeBergstrand
closed
10 months ago
3
Additional Flags to Run_One
#51
LeeBergstrand
opened
10 months ago
2
Update dependancy versions
#50
LeeBergstrand
opened
10 months ago
0
Update readme to reflect new CLI and install.
#49
LeeBergstrand
closed
6 months ago
1
End repair
#48
jmtsuji
closed
10 months ago
1
Modify python scripts so they can be called directly rather than downloaded.
#47
LeeBergstrand
closed
10 months ago
10
Add Lee's code (CLI + Various Fixes) to develop.
#46
LeeBergstrand
closed
10 months ago
1
Create Rotary Download CLI Command
#45
LeeBergstrand
opened
10 months ago
5
Add snakemake subprocess
#44
LeeBergstrand
closed
10 months ago
0
Modify the workflow to add multi-sample capability
#43
LeeBergstrand
closed
10 months ago
3
Add Conda install and register package with anaconda.
#42
LeeBergstrand
opened
10 months ago
4
Create auto install of all code and CLI
#41
LeeBergstrand
closed
10 months ago
2
Call existing Snakemake workflow from the CLI
#40
LeeBergstrand
closed
10 months ago
1
Create CLI
#39
LeeBergstrand
closed
10 months ago
5
Add automated Illumina QC (similar to ATLAS).
#38
LeeBergstrand
closed
9 months ago
5
Add genome coverage and depth calculations for both nanopore and illumina.
#37
LeeBergstrand
closed
10 months ago
1
Add CheckM for genome completeness calculation
#36
LeeBergstrand
closed
10 months ago
3
Bug fixes lee
#35
LeeBergstrand
closed
11 months ago
0
Bug fixes lee
#34
LeeBergstrand
closed
11 months ago
0
Bug fixes lee
#33
LeeBergstrand
closed
11 months ago
2
GTDB download version is hard coded.
#32
LeeBergstrand
closed
11 months ago
5
GTDBtk fails to due to prodigal's Non-Zero exit code.
#31
LeeBergstrand
closed
11 months ago
9
Default Egg Nog Mapper Mode
#30
LeeBergstrand
closed
11 months ago
4
PFAM website is being shutdown. Start HMM can no longer be downloaded.
#29
LeeBergstrand
closed
10 months ago
12
Rotary fails silently on rule repair_ends (addressed by creation of repair.py)
#28
LeeBergstrand
closed
10 months ago
5
Snakemake can't find sequencing files if --directory output_dir is used.
#27
LeeBergstrand
closed
11 months ago
2
Merge End Repair into Develop
#25
LeeBergstrand
closed
11 months ago
2
Sync Main and Develop
#24
LeeBergstrand
closed
11 months ago
0
Rotary CLI
#23
jmtsuji
closed
4 months ago
8
Update README
#22
jmtsuji
closed
1 year ago
0
Circularization and polishing stand alone script?
#21
gwl2
closed
4 months ago
2
Bump version
#20
jmtsuji
closed
1 year ago
0
Handle circularization edge case
#19
jmtsuji
closed
1 year ago
0
Bump medaka version
#18
jmtsuji
closed
1 year ago
1
Fix read_error support for flye_end_repair.sh
#17
jmtsuji
closed
1 year ago
0
Task list for rotary
#15
jmtsuji
closed
4 months ago
2
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