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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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Improve Documentation For aggregate_contigs in circularize.smk
#151
LeeBergstrand
opened
3 months ago
0
Change the contig info file added to the stats folder
#150
jmtsuji
closed
3 months ago
1
Optimize medaka parallelization contig manifest
#149
LeeBergstrand
closed
3 months ago
0
Optimize medaka parallelization by contig
#148
LeeBergstrand
closed
3 months ago
0
Optimize medaka parallelization
#147
LeeBergstrand
closed
3 months ago
5
Allow for no short read input
#146
LeeBergstrand
closed
3 months ago
1
Develop lee
#145
LeeBergstrand
closed
2 months ago
3
Make compatible with pungi updates
#144
LeeBergstrand
closed
3 months ago
0
Make compatible with pungi updates
#143
LeeBergstrand
closed
3 months ago
1
Get gtdbtk to use dfast proteins as input.
#142
LeeBergstrand
closed
2 months ago
3
Catch up stitch_module with develop
#141
jmtsuji
closed
4 months ago
0
Make annotation sub-rules optional
#140
jmtsuji
closed
2 months ago
4
Re-consider the symlinking paradigm used in rotary
#139
jmtsuji
opened
4 months ago
0
move keep_final_qc_read_files to true.
#138
LeeBergstrand
closed
4 months ago
0
Move to using pungi for the sample and snakemake CLI management code.
#137
LeeBergstrand
closed
4 months ago
3
Clean up install code
#136
LeeBergstrand
closed
4 months ago
0
Replace POLCA with pypolca
#135
jmtsuji
closed
4 months ago
6
Pipeline tries to re-run from QC when re-started
#134
jmtsuji
opened
4 months ago
0
Update pypolca branch to latest develop
#133
jmtsuji
closed
4 months ago
0
QC read files deleted too early
#132
jmtsuji
opened
4 months ago
24
Better parallelization for medaka
#131
jmtsuji
closed
2 months ago
4
Optionally keep final QC reads
#130
jmtsuji
closed
4 months ago
0
Add flag to keep final QC read files
#129
jmtsuji
closed
4 months ago
2
Rewrite certain sections of the documentation for improved readability.
#128
LeeBergstrand
closed
4 months ago
1
Minor README updates
#127
jmtsuji
closed
4 months ago
4
Fix coverage summary
#126
jmtsuji
closed
4 months ago
3
Improve read mapping rules
#125
LeeBergstrand
closed
4 months ago
7
Simplify read mapping file extension code in rules.
#124
LeeBergstrand
closed
4 months ago
1
Breakout polypolish read mapping to its own rule.
#123
LeeBergstrand
closed
4 months ago
1
Install Polypolish via Conda
#122
LeeBergstrand
closed
4 months ago
6
Update stitch_module branch
#121
jmtsuji
closed
4 months ago
0
Simplify Python code within certain snakemake rules
#120
jmtsuji
opened
4 months ago
6
Add flag to keep read coverage mapping BAM files.
#119
LeeBergstrand
closed
4 months ago
1
Allow long read-only with when polish_with_short_reads set to 'False'.
#118
LeeBergstrand
closed
2 months ago
3
Make repair.py generate repair_info.tsv with linear contigs.
#117
LeeBergstrand
closed
5 months ago
0
Repair.py fails to write repair_info.tsv when no circular contigs are identified by Flye.
#116
LeeBergstrand
closed
5 months ago
3
Refactor sample
#115
LeeBergstrand
closed
5 months ago
0
Develop lee
#114
LeeBergstrand
closed
4 months ago
8
Refactor snakefile
#113
LeeBergstrand
closed
5 months ago
0
Refactor cli
#112
LeeBergstrand
closed
5 months ago
0
Move to Snakemake 8.0
#111
LeeBergstrand
opened
6 months ago
1
Refactor snakefile
#110
LeeBergstrand
closed
5 months ago
2
add Split snakefile
#109
LeeBergstrand
closed
6 months ago
0
update temp files with split snakemake files
#108
LeeBergstrand
closed
6 months ago
0
Update more_temp_files
#107
LeeBergstrand
closed
6 months ago
0
Hot-Fix Polca
#106
LeeBergstrand
closed
6 months ago
0
Hot-Fix Fix Polca
#105
LeeBergstrand
closed
6 months ago
0
split snakemake file into multiple.
#104
LeeBergstrand
closed
6 months ago
1
Add software demo to README
#103
jmtsuji
closed
6 months ago
0
Misc changes
#102
LeeBergstrand
closed
6 months ago
3
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