issues
search
EPPIcenter
/
mad4hatter
https://eppicenter.github.io/mad4hatter/
5
stars
13
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
temporary fix for cutadapt, two rounds, seconf is a for loop
#161
bgpalmer
opened
1 month ago
0
Remove testdata from repo and alter path in help message
#160
kathryn1995
opened
1 month ago
0
Update targets to pools
#159
kathryn1995
opened
2 months ago
0
Sequencer values
#158
jodyphelan
opened
3 months ago
1
Update resources
#157
kathryn1995
closed
3 months ago
0
use unique asv and locus to align against reference
#156
bgpalmer
closed
3 months ago
0
Make sequencer mandatory input
#155
kathryn1995
closed
3 months ago
0
Update res marker module
#154
kathryn1995
closed
3 months ago
7
max EE changed to 3 and commented code removed from dada script
#153
kathryn1995
closed
3 months ago
0
use zgrep to get amplicon counts
#152
bgpalmer
closed
3 months ago
0
fix typo
#151
bgpalmer
closed
3 months ago
0
only run cigar build on unique refseq and hapseq combinations
#150
kathryn1995
closed
4 months ago
1
col names in dada2.clusters.txt
#149
andres-ad
opened
4 months ago
2
misspelling demultiplexed in work folder
#148
andres-ad
opened
5 months ago
0
Add default for help to prevent warning showing
#147
kathryn1995
closed
4 months ago
0
initialize help parameter variable
#146
bgpalmer
closed
5 months ago
0
Add help message
#145
kathryn1995
closed
5 months ago
0
use correct key in cutadapt json report for reporting number of ampli…
#144
bgpalmer
closed
5 months ago
2
Add help message
#143
kathryn1995
closed
5 months ago
1
Check-in script to check panel definitions. Additionally, update pipe…
#142
bgpalmer
opened
5 months ago
2
Add v5 resources
#141
kathryn1995
closed
5 months ago
1
Add v4 reference which has all loci including species
#140
kathryn1995
closed
4 months ago
0
add missed channel variable declarations
#139
bgpalmer
closed
6 months ago
0
Update documentation for masking parameters and resource documentation
#138
bgpalmer
closed
6 months ago
0
add resource tier to coverage files
#137
bgpalmer
closed
6 months ago
0
Update locus and add interpretation info
#136
kathryn1995
closed
6 months ago
0
bump manifest config version v0.1.9 -> v0.2.1
#135
bgpalmer
closed
6 months ago
0
change results folder from dada2_analysis to raw_dada2_output
#134
bgpalmer
closed
7 months ago
0
Include post-dada2 collapse module into the postprocessing module
#133
bgpalmer
closed
7 months ago
1
Update exec and environments
#132
bgpalmer
closed
4 months ago
1
Update dada2 to pseudo pooling and format dada_overlaps.R
#131
kathryn1995
closed
7 months ago
0
Fix positions for incorrect markers and remove ones not in amplicon
#130
kathryn1995
closed
7 months ago
1
DADA2 memory optimizations and bugfixes
#129
m-murphy
closed
9 months ago
1
Remove code that replaces insertion in reference with N
#128
kathryn1995
closed
9 months ago
1
add note that the resistance marker module can only be run with the v…
#127
bgpalmer
closed
10 months ago
0
Updates to allow the pipeline to run using older versions of the pane…
#126
bgpalmer
closed
10 months ago
1
Add documentation for the postprocessing only module
#125
bgpalmer
closed
10 months ago
2
allow postprocessing modules to be run separately
#124
bgpalmer
closed
11 months ago
1
allow resistance marker tables to show locus level granularity
#123
bgpalmer
closed
7 months ago
7
remove duplicate entry in resmarker table
#122
bgpalmer
closed
1 year ago
0
record params + update alleletable column headers
#121
bgpalmer
closed
1 year ago
0
revert last erroneous commit
#120
manuelgug
closed
1 year ago
0
Off by one fix
#119
bgpalmer
closed
1 year ago
0
OutputDada2 and OutputPostprocessing in sample_coverage.txt have NAs, should have 0 for consistency
#118
bgpalmer
closed
1 year ago
1
Look for potential optimizations during trimAndFilter + PhiX removal
#117
bgpalmer
opened
1 year ago
0
Inlcude pool2 resmarker
#116
bgpalmer
closed
1 year ago
0
Refactor dada
#115
bgpalmer
closed
1 year ago
3
dada2 parallelization support
#114
m-murphy
closed
1 year ago
2
Resmarker mask fix
#113
bgpalmer
closed
1 year ago
0
missed substitutions are included with unit tests
#112
bgpalmer
closed
1 year ago
0
Next