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reichlab
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cladetime
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https://cladetime.readthedocs.io
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A few documentation tweaks
#38
bsweger
closed
1 day ago
2
In unscored-location-dates, use two-letter abbreviations for states to match variant nowcast hub convention
#37
elray1
opened
4 days ago
1
Missing date values
#36
elray1
opened
4 days ago
0
Add readthedocs and sphinx to cladetime
#35
bsweger
closed
1 day ago
1
Update CladeTime tree_as_of and sequence_as_of date handling
#34
bsweger
closed
1 week ago
0
Update timestamp validations when instantiating CladeTime class
#33
bsweger
closed
1 week ago
0
Rename package to cladetime
#32
bsweger
closed
1 week ago
0
Rename virus-clade-utils to cladetime
#31
bsweger
closed
1 week ago
0
Create initial documentation for the CladeTime class in virus-clade-utils
#30
bsweger
closed
1 day ago
0
Improvements to logging and timing
#29
bsweger
closed
1 week ago
0
Add a CladeTime method to return an "as_of" reference tree
#28
bsweger
opened
2 weeks ago
1
Add a sequence_metadata attribute to CladeTime
#27
bsweger
closed
2 weeks ago
0
Add function to retrieve metadata from Nextstrain's ncov pipeline run at a specific point in time
#26
bsweger
closed
2 weeks ago
0
double quote to single inside fstring
#25
elray1
closed
3 weeks ago
0
Incorporate timestamp when using an "as_of" date to get the VersionID of an S3 object
#24
bsweger
opened
3 weeks ago
0
Bsweger/metadata download as of
#23
bsweger
closed
3 weeks ago
3
Add S3 VersionId parameter to virus-clade-utils function that downloads sequence metadata from Nexstrain
#22
bsweger
closed
3 weeks ago
1
Include Puerto Rico when filtering Nextstrain metadata
#21
bsweger
closed
1 month ago
0
Add a function to get metadata for the latest Nextclade ncov-ingest pipeline
#20
bsweger
closed
2 weeks ago
0
Get genome sequence and its metadata by downloading Nextstrain files instead of via the NCBI API
#19
bsweger
opened
1 month ago
0
Bsweger/get clades list
#18
bsweger
closed
1 month ago
1
First pass at bringing in code from clade_data_utils
#17
bsweger
closed
1 month ago
1
Add instructions for running tests in docker
#16
bsweger
closed
1 month ago
0
Move data_utils functions to virus-clade-utils
#13
bsweger
closed
1 month ago
0
Create a function to retrieve Nextclade ncov-ingest pipeline metadata at a point in time
#12
bsweger
closed
3 weeks ago
1
Finalize the format of the target data
#11
bsweger
opened
2 months ago
0
Bsweger/align with nextstrain
#10
bsweger
closed
1 month ago
0
Provide a way to automate local dev setup
#9
bsweger
closed
1 month ago
3
Update usage of Nextstrain tools based on latest information
#8
bsweger
closed
1 month ago
0
variant data pipeline: replicate any metadata cleanup steps done by Bedford group
#1
elray1
closed
3 weeks ago
1
Try an alternate workflow for getting the COVID reference tree for a specific date
#7
bsweger
closed
2 months ago
2
target data pipeline: update nextclade CLI to 3.8 or greater
#2
bsweger
closed
2 months ago
1
Determine pipeline behavior when/if any downloaded sequences do not have corresponding metadata
#3
bsweger
opened
5 months ago
0
use root sequence obtained via nextstrain
#4
bsweger
closed
2 months ago
2
catch and fail early on errors in downloading data
#5
elray1
closed
3 weeks ago
2
Add support to specify the start and end of a date range for sequence collection dates
#6
elray1
opened
5 months ago
3