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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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Add viral read extraction and visualisation
#119
colindaven
closed
3 years ago
0
extract viral reads from bam
#118
colindaven
closed
3 years ago
2
Add new clost bot e ref
#117
colindaven
closed
3 years ago
0
run haybaler just for one type of rep.csv
#116
poer-sophia
closed
3 years ago
0
postprocess and haybaler - too many files ?
#115
colindaven
closed
3 years ago
4
Add MQ20 option, use ref.tmp
#114
colindaven
closed
3 years ago
0
last refseq used
#113
colindaven
closed
3 years ago
2
detect local conda dynamically in bash, and source
#112
colindaven
closed
3 years ago
1
add mapping quality 20 mq20 option
#111
colindaven
closed
3 years ago
1
New 2021 references
#110
colindaven
closed
3 years ago
0
docs - add postprocess and haybaler
#109
colindaven
closed
3 years ago
1
Add wochenende_plot.sh update.Minor changes, fixed wochenende_preprocess bug
#108
colindaven
closed
3 years ago
0
updated wochenende_plot
#107
poer-sophia
closed
3 years ago
0
Add "proper" HTML documentation
#106
B1T0
closed
3 years ago
3
Added bacterial genomes and bumped postproc to 0.14
#105
colindaven
closed
3 years ago
1
Added genome references
#104
poer-sophia
closed
3 years ago
0
Update reporting, wochenende_postprocess and lint
#103
colindaven
closed
3 years ago
0
merges
#102
colindaven
closed
3 years ago
0
Add ecoli, update wochenende_postprocess.sh
#101
colindaven
closed
3 years ago
2
environment - rebuild for haybaler
#100
colindaven
closed
3 years ago
0
Add shell argument checks
#99
colindaven
closed
3 years ago
0
check lambda phage reads in ONT
#98
colindaven
opened
3 years ago
0
Merge initial wochenende_postprocess script
#97
colindaven
closed
3 years ago
1
v1.8.1 swap mq30 task towards end so can be better compared
#96
colindaven
closed
3 years ago
0
mq30 step - set towards end of process so can exclude
#95
colindaven
closed
3 years ago
1
add merges
#94
colindaven
closed
3 years ago
0
Add schematic, tutorial minor update, create omitted bam.bai
#93
colindaven
closed
3 years ago
0
mapping stats - revise for PE reads
#92
colindaven
opened
3 years ago
0
Redesign and revise tests
#91
colindaven
opened
3 years ago
2
Add 1.8, fixmates, name sorting for PE read dup calling
#90
colindaven
closed
3 years ago
5
Merge non-prinseq default, remove RPMM bug, improve sambamba depth
#89
colindaven
closed
3 years ago
0
PE reads - unmapped sequences not output
#88
colindaven
opened
4 years ago
0
Try creating minimal conda environment
#87
colindaven
closed
3 years ago
1
add samtools fixmate for PE reads
#86
colindaven
closed
3 years ago
2
no_prinseq may interfere with .ndp. step perldup
#85
colindaven
closed
4 years ago
1
wochenende plot error b: exotic headers ?
#84
colindaven
closed
3 years ago
3
bug in RPMM calculation
#83
colindaven
closed
4 years ago
0
Add massiveref 2020_09, move cleanup and test scripts to subdir
#82
colindaven
closed
4 years ago
1
fix bug in RPMM calculation, and round to 5 digits after point or comma
#81
sannareddyk
closed
4 years ago
2
basic_reporting.py and conda on ngsnfs
#80
sannareddyk
closed
3 years ago
0
docs updates
#79
colindaven
closed
4 years ago
0
update dev
#78
colindaven
closed
4 years ago
0
trim_galore trimming considerations
#77
colindaven
closed
3 years ago
1
Add trim_galore (tested) and updated conda env (untested)
#76
colindaven
closed
4 years ago
1
create new repo for conda env yml comparisons
#75
colindaven
closed
4 years ago
1
Add flexible mismatch logic for long reads
#74
colindaven
closed
4 years ago
0
Dev - add ngmlr long read alignment changes
#73
colindaven
closed
4 years ago
0
set ngmlr parameters
#72
colindaven
closed
4 years ago
2
complete nextera adapter removal improvements: add trim-galore
#71
colindaven
closed
4 years ago
1
perl version mismatch
#70
sannareddyk
closed
4 years ago
2
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