issues
search
CVUA-RRW
/
FooDMe
A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.
https://cvua-rrw.github.io/FooDMe
BSD 3-Clause "New" or "Revised" License
4
stars
1
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
MIDORI
#69
gregdenay
closed
6 months ago
0
[Request] Lock Blast DB Version
#68
marchoeppner
opened
6 months ago
1
Add option to deactivate the BLAST default DUST filter for low complexity sequences
#67
gregdenay
closed
10 months ago
0
Add option to switch from 'megablast' to 'blastn'
#66
gregdenay
closed
10 months ago
1
Fix for `trim_primers_3end` parameter and primer sequences containing ambiguous nucleotides
#65
gregdenay
closed
1 year ago
0
[BUG] Incorrect parsing of the `trim_primers_3end` parameter
#64
gregdenay
closed
1 year ago
0
[BUG] Ambiguous characters in Primer sequences are not treated as such
#63
gregdenay
closed
1 year ago
1
Ion torrent sequences
#62
rentper93
closed
6 months ago
2
How can I use this workflow for Illumina single-end data?
#61
adimascf
closed
1 year ago
2
[Request] Exclude specific sequences from the nucleotide database based on SeqID
#60
gregdenay
closed
1 year ago
1
[Request] Organism name in Benchmarking report
#59
gregdenay
closed
1 year ago
1
Fixing benchmark rule
#58
gregdenay
closed
2 years ago
0
Adding paramspace exploration helper
#57
gregdenay
closed
2 years ago
0
Software versions missing
#56
gregdenay
closed
2 years ago
1
Missing error values
#55
gregdenay
closed
2 years ago
1
Benchmarking
#54
gregdenay
closed
2 years ago
0
Bug fix
#53
gregdenay
closed
2 years ago
0
Use of bc bash calculator causes compatibility problems on some distributions
#52
gregdenay
closed
2 years ago
1
clone counter
#51
gregdenay
closed
2 years ago
0
clone counter
#50
gregdenay
closed
2 years ago
0
Fixed unskipped header in consensus determination script
#49
gregdenay
closed
2 years ago
0
fix individual reports
#48
gregdenay
closed
2 years ago
0
update doc
#47
gregdenay
closed
2 years ago
0
first draft of site structure
#46
gregdenay
closed
2 years ago
0
extend testing to macOS
#45
gregdenay
closed
2 years ago
1
Foodme environment error
#44
gregdenay
closed
2 years ago
3
Patch 1.4.6
#43
gregdenay
closed
2 years ago
0
Rule prep_taxonomy fails in 1.4.5
#42
gregdenay
closed
2 years ago
0
Calculation of components concentration
#41
gregdenay
closed
2 years ago
0
soft derpecation of the python wrapper
#40
gregdenay
closed
2 years ago
1
Dada error handling
#39
gregdenay
closed
2 years ago
0
Linting
#38
gregdenay
closed
2 years ago
0
update environements
#37
gregdenay
closed
2 years ago
1
Deploy with minimal env requirements
#36
gregdenay
closed
2 years ago
1
Fix pandas CopyWarning
#35
gregdenay
closed
2 years ago
2
Snakemake version
#34
gregdenay
closed
2 years ago
1
Outdated BLAST+ version
#33
gregdenay
closed
2 years ago
1
Better error catching for Dada
#32
gregdenay
closed
2 years ago
1
Panda CopyWarning
#31
gregdenay
closed
2 years ago
1
Documentation
#30
gregdenay
closed
2 years ago
1
Remove wrapper
#29
gregdenay
closed
2 years ago
1
Move long shell or python blocks to scripts.
#28
gregdenay
closed
2 years ago
1
Implement organized and usefull logging
#27
gregdenay
closed
2 years ago
1
Linting
#26
gregdenay
closed
2 years ago
0
Taxonomy dump files are now parsed only once
#25
gregdenay
closed
2 years ago
0
Implementing a blocklist system for unwanted taxids.
#24
gregdenay
closed
2 years ago
0
Patch 12
#23
gregdenay
closed
2 years ago
0
fixed calculation of sequences discarded after primer trimming
#22
gregdenay
closed
2 years ago
0
Updated readme
#21
gregdenay
closed
2 years ago
0
Upgrade taxidTools to version 2
#20
gregdenay
closed
2 years ago
1
Next