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COG-UK
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datapipe
Nextflow implementation of grapevine
GNU General Public License v3.0
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changes to reinstall on grinch
#40
rmcolq
closed
1 month ago
0
GISAID JSON DUMP
#39
leke-lyu
opened
11 months ago
2
Handle upcoming pangolin 4.0 changes
#38
rmcolq
opened
2 years ago
0
Add geography module
#37
rmcolq
closed
2 years ago
0
Move geography cleaning to its own module
#36
rmcolq
closed
2 years ago
1
Dev
#35
rmcolq
closed
3 years ago
0
Dev
#34
rmcolq
closed
3 years ago
0
Create civet3 outputs
#33
rmcolq
closed
3 years ago
0
Merge in new utla output and deduplication fix for metadata
#32
rmcolq
closed
3 years ago
0
Duplicate entries in cog_metadata.csv, some with differing lineages
#31
AngieHinrichs
closed
3 years ago
2
Move s3 out of datapipe
#30
rmcolq
closed
3 years ago
1
Add optional gisaid-only geography cleaning
#29
rmcolq
closed
3 years ago
0
Add output file for use by pango-designation projects
#28
rmcolq
closed
3 years ago
1
Handle samples with mostly missing metadata
#27
rmcolq
closed
3 years ago
1
Update geography cleaning with global adm1 cleaning
#26
rmcolq
closed
3 years ago
0
Make boolean columns have Y/N values consistent with majora
#25
rmcolq
closed
3 years ago
0
Update `pillar_2` to `is_pillar_2`
#24
rmcolq
closed
3 years ago
0
Remove mutations which are specifically typed
#23
rmcolq
closed
3 years ago
1
Force overwrite adm2
#22
rmcolq
closed
3 years ago
0
Investigate disappearing sequences
#21
rmcolq
closed
3 years ago
1
Create COG epi metadata file
#20
rmcolq
closed
3 years ago
1
Add columns to consortium metadata
#19
rmcolq
closed
3 years ago
3
Take in phylopipe2 metadata with `uk_lineages` as previous metadata
#18
rmcolq
closed
3 years ago
1
Handle incoming pangolin updates
#17
rmcolq
closed
3 years ago
0
Pass `uk_lineage` through from previous metadata if possible
#16
rmcolq
closed
3 years ago
0
Update pangolin columns which pass through to outputs
#15
rmcolq
closed
3 years ago
0
Reaching sequence divergence threshold where minimap2 will fail to align new sequences to reference
#14
rmcolq
closed
3 years ago
1
Add safe latitude/longitude to unlinked file output
#13
rmcolq
closed
2 years ago
1
Add a workflow for grinch website
#12
rmcolq
closed
3 years ago
0
Add gisaid preprocessing and an all datapipe
#11
rmcolq
closed
3 years ago
0
Add gisaid preprocessing pipeline
#10
rmcolq
closed
3 years ago
1
Add resource requirements where necessary
#9
rmcolq
closed
3 years ago
1
Check is robust to missing (non-required) input files
#8
rmcolq
opened
3 years ago
0
Make `combine_variants` process robust to different columns in the two input files
#7
rmcolq
closed
3 years ago
1
Move workflows out of module files into their own files
#6
rmcolq
opened
3 years ago
0
No command line help
#5
rmcolq
opened
3 years ago
0
Cannot find resource files unless run from github repo directory
#4
rmcolq
opened
3 years ago
0
try to get publish working in parallel
#3
rmcolq
closed
3 years ago
0
Updated dedup and metadata choices
#2
rmcolq
closed
3 years ago
0
Track when samples dropped
#1
rmcolq
closed
3 years ago
0