issues
search
NMRL
/
Ardetype
Pipeline allows to perform reference-guided de-novo assembly of bacterial genomes, starting from Illumina PE150 fastq files.
1
stars
0
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
CRUD operations based on tags
#40
omegatro
opened
8 months ago
0
Timestamp fix
#39
omegatro
closed
7 months ago
1
Shigatyper
#38
omegatro
closed
8 months ago
1
Shigatyper
#37
omegatro
closed
8 months ago
1
Sample identifiers
#36
omegatro
opened
8 months ago
7
CICD for up to date external dependencies
#35
omegatro
opened
8 months ago
0
Cgmlst schemas curration
#34
omegatro
opened
8 months ago
4
History file filters, dates and uniqueness determinants
#33
omegatro
closed
8 months ago
1
Spatyper aggregation
#32
omegatro
closed
9 months ago
0
Virulencefinder
#31
omegatro
closed
9 months ago
0
Add virulencefinder
#30
omegatro
closed
8 months ago
1
Ardetype wrapper
#29
omegatro
opened
10 months ago
0
Aggregation refactoring
#28
omegatro
closed
10 months ago
0
Aquamis qc
#27
omegatro
closed
11 months ago
0
AQUAMIS qc criteria integration
#26
omegatro
closed
11 months ago
3
CMD argument to force rerun of specific rules
#25
omegatro
closed
11 months ago
1
Add logic to the wrapper to deal with common processing fails
#24
omegatro
opened
11 months ago
1
Chewbbaca versioning
#23
omegatro
closed
11 months ago
1
Persample tool report
#22
omegatro
closed
11 months ago
1
Merge outputs
#21
omegatro
closed
11 months ago
0
Per-sample software logs
#20
omegatro
closed
11 months ago
1
Backing-up aggregation scripts
#19
omegatro
closed
11 months ago
0
Added settings for Streptococcus pyogenes cgmlst
#18
omegatro
closed
11 months ago
0
Transfer cgmlst database settings to config file from bact_tip
#17
omegatro
closed
11 months ago
2
Add cgmlst schema for S.pyogenes
#16
omegatro
closed
11 months ago
1
Chewbbaca quality
#15
omegatro
closed
11 months ago
0
Add database aggregation for lrefinder.
#14
omegatro
closed
10 months ago
2
Added code to aggregate lrefinder_output
#13
omegatro
closed
11 months ago
0
Lrefinder report
#12
omegatro
closed
11 months ago
0
Add database aggregation for chewbbaca quality.
#11
omegatro
closed
10 months ago
2
Added cgmlst database for Clostridioides difficile.
#10
omegatro
closed
11 months ago
0
Add chewbbaca quality metric aggregation under report folder
#9
omegatro
closed
11 months ago
3
Integrate cgmlst database for Clostridioides difficile for chewbbaca.
#8
omegatro
closed
11 months ago
1
Provide a way to reliably combine outputs from different analyses
#7
omegatro
closed
11 months ago
2
Add aggregation for stecfinder under reports
#6
omegatro
closed
11 months ago
0
Add aggregation for LRE-Finder output under reports
#5
omegatro
closed
11 months ago
1
Lre finder
#4
omegatro
closed
11 months ago
0
Look for ways to add sccmecfinder from https://cge.food.dtu.dk/services/SCCmecFinder-1.1/ or extend the output of https://github.com/staphopia/staphopia-sccmec
#3
omegatro
opened
11 months ago
0
Problem related to https://github.com/snakemake/snakemake/issues/759 when main script sits idle if left unchecked under screen.
#2
omegatro
opened
11 months ago
0
Add LRE_finder from https://bitbucket.org/genomicepidemiology/lre-finder/src/master/
#1
omegatro
closed
11 months ago
1