issues
search
NBISweden
/
aMeta
Ancient microbiome snakemake workflow
MIT License
19
stars
15
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Pr actions
#73
percyfal
closed
1 year ago
0
Explicitly list pr branch in actions
#72
percyfal
closed
1 year ago
0
Rule PMD_score failing with no error message
#71
ZoePochon
closed
1 year ago
6
Add -p to mkdir in case folder exists
#70
ZoePochon
closed
1 year ago
0
switch to abundance quantification in python
#69
clami66
closed
1 year ago
2
The Malt_QuantifyAbundance rule takes la long time to run
#68
clami66
closed
1 year ago
0
Add rule name to messages and number to PMD_scores
#67
percyfal
closed
2 years ago
0
Add flag --number 100000 to the PMDtools rule
#66
ZoePochon
closed
2 years ago
0
Use rule names verbatim in messages
#65
percyfal
closed
2 years ago
0
checkpoint rules produce different amount of outputs depending on target type
#64
percyfal
closed
2 years ago
1
Malt_Extract fails due to missing entries in custom ncbi.map
#63
percyfal
closed
1 year ago
1
Post_Processing rule fails due to missing input data?
#62
percyfal
closed
2 years ago
1
Erroneous combinations of taxid and refids
#61
percyfal
closed
2 years ago
1
Some interesting microbes are ignored because they are labelled as "no rank" in the ncbi database
#60
ZoePochon
opened
2 years ago
3
Add ref_id to outputs
#59
percyfal
closed
2 years ago
0
seqtk subseq is slow on large databases
#58
clami66
closed
1 year ago
1
Make authentication bash script into snakemake workflow
#57
clami66
closed
2 years ago
3
Authentication might fail depending on MaltExtract output
#56
clami66
closed
7 months ago
14
parameterized breadth and depth of coverage filters for krakenuniq
#55
LeandroRitter
closed
2 years ago
0
Disregard errors from postprocessing.AMPS.r
#54
percyfal
closed
2 years ago
0
Parameter `in_dir` is unused in `scripts/authentic.R`
#53
clami66
closed
2 years ago
1
sample names and fastqc
#52
percyfal
closed
1 month ago
2
Fix argument ten
#51
percyfal
closed
2 years ago
0
Remap envmodules key names
#50
percyfal
closed
2 years ago
1
envmodules configuration sections should follow conda environment files
#49
percyfal
closed
2 years ago
8
Authentic threads
#48
percyfal
closed
2 years ago
0
envmodules section is missing in Authentication rule
#47
clami66
closed
2 years ago
1
Print commands in workflow test
#46
percyfal
closed
2 years ago
0
Adapt number of threads in authentication script
#45
clami66
closed
2 years ago
1
added envmodules config file
#44
clami66
closed
2 years ago
0
added database paths for runs on real data
#43
LeandroRitter
closed
2 years ago
0
Kronadb
#42
clami66
closed
2 years ago
0
Move module configuration to a separate config file
#41
clami66
closed
2 years ago
2
added rma-tabuliser
#40
LeandroRitter
closed
2 years ago
0
added rma-tabuliser
#39
LeandroRitter
closed
2 years ago
0
added rma-tabuliser
#38
LeandroRitter
closed
2 years ago
0
added rma-tabuliser
#37
LeandroRitter
closed
2 years ago
0
added rma-tabuliser
#36
LeandroRitter
closed
2 years ago
0
added rma-tabuliser
#35
LeandroRitter
closed
2 years ago
0
fixed duplicate sequence in header error in authentication
#34
LeandroRitter
closed
2 years ago
0
Use option -a2t for malt-build for version compatibility
#33
percyfal
closed
2 years ago
1
Add function to check authentication exit codes
#32
percyfal
closed
2 years ago
0
Add fixes to authentication step
#31
percyfal
closed
2 years ago
0
fixed authntication step
#30
LeandroRitter
closed
2 years ago
0
fixed authentication step
#29
LeandroRitter
closed
2 years ago
0
fixed authentication step
#28
LeandroRitter
closed
2 years ago
0
fixed authentication step
#27
LeandroRitter
closed
2 years ago
0
Add mapdamage index
#26
percyfal
closed
2 years ago
0
replaced malt with hops in main.yaml
#25
LeandroRitter
closed
2 years ago
0
fixed indentation issue in damage.smk
#24
LeandroRitter
closed
2 years ago
0
Previous
Next