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MHH-RCUG
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Wochenende
Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
https://github.com/MHH-RCUG/nf_wochenende
MIT License
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growth rate fine tuning
#169
colindaven
closed
3 years ago
0
growth rate - exclude 1,2,3,4 etc
#168
colindaven
closed
3 years ago
1
growth rate problems
#167
colindaven
closed
3 years ago
3
solved Error Could not find expected file
#166
poer-sophia
closed
3 years ago
0
add two new ref seqs
#165
colindaven
closed
3 years ago
0
update config for trimmomatic
#164
colindaven
closed
3 years ago
0
truseq PE in SE ...
#163
colindaven
closed
3 years ago
1
add pe mode - bai for dup.bam
#162
colindaven
closed
3 years ago
0
growth rate naming and submission improvements
#161
colindaven
closed
3 years ago
0
Add growth rate code , update postprocess
#160
colindaven
closed
3 years ago
0
add useSLURM to config.yaml
#159
colindaven
closed
2 years ago
1
speedup growth rates
#158
colindaven
closed
3 years ago
5
Supply bam.txt and bam.bai file as links.
#157
colindaven
closed
3 years ago
0
update dev
#156
colindaven
closed
3 years ago
0
minimap bump 2.21
#155
colindaven
closed
3 years ago
1
conda env improvements, testing, plot srun speedup
#154
colindaven
closed
3 years ago
4
python3.7 env error: TypeError: 'LineCollection' object is not iterable
#153
colindaven
closed
3 years ago
4
integrate raspir as module
#152
colindaven
closed
2 years ago
1
update conda env, update docs
#151
colindaven
closed
3 years ago
0
new minimal wochenende env for python 3.7
#150
colindaven
closed
3 years ago
0
plot - change dependencies with python3.7
#149
colindaven
closed
3 years ago
3
bedtools
#148
poer-sophia
closed
3 years ago
2
Add Toms growth rate code
#147
colindaven
closed
3 years ago
0
postprocess log full of "processing rederence"
#146
poer-sophia
closed
3 years ago
1
growth rate code integration
#145
colindaven
closed
3 years ago
8
Add growth rate code
#144
poer-sophia
closed
3 years ago
0
NM bamtools curiosity : a few reads slip through
#143
colindaven
opened
3 years ago
1
use featureCounts or htseq-count instead of samtools idxstats for counting ?
#142
colindaven
closed
2 years ago
1
wrap plot in srun for faster plot generation
#141
colindaven
closed
3 years ago
2
reduce bash scripts to single script with functions
#140
colindaven
opened
3 years ago
0
config, yaml, output log for postprocess
#139
colindaven
closed
3 years ago
1
Add new config yaml and setup.sh changes to dev
#138
colindaven
closed
3 years ago
1
testing branch config
#137
colindaven
closed
3 years ago
6
KeyError
#136
colindaven
closed
3 years ago
0
new wochenende env: python3.6 EOL Dec 2021
#135
colindaven
closed
3 years ago
21
merge master into config
#134
colindaven
closed
3 years ago
0
tests by Tobias, SFB reference added
#133
colindaven
closed
3 years ago
0
bump minimap2 2.2.20
#132
colindaven
closed
3 years ago
1
tests
#131
colindaven
opened
3 years ago
0
postprocess - check dependencies at start before running
#130
colindaven
opened
3 years ago
0
Testing with pytest
#129
B1T0
closed
3 years ago
3
1.9.5 add minimap2short aligner
#128
colindaven
closed
3 years ago
0
update seqres paths
#127
colindaven
closed
3 years ago
0
Merge in your fork ?
#126
colindaven
closed
3 years ago
2
Configuration Management: Paths, etc.
#125
B1T0
closed
3 years ago
11
Add --no-plot mode to speed up postprocess
#124
colindaven
closed
3 years ago
1
postprocess - add --no-plots option
#123
colindaven
closed
3 years ago
1
Add AlignerBoost - relatively untested
#122
colindaven
closed
3 years ago
0
1.9.2 solve ref.tmp error handling
#121
colindaven
closed
3 years ago
0
Docs and tutorial updates
#120
colindaven
closed
3 years ago
0
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