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CDPHE-bioinformatics
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CDPHE-SARS-CoV-2
Workflows and scripts for the assembly and analysis of SARS-CoV-2 whole genome tiled amplicon sequencing.
https://cdphe-bioinformatics.github.io/CDPHE-SARS-CoV-2/
GNU General Public License v3.0
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[BUG] Invalid escape sequence in newer versions of python
#31
danpolanco
opened
3 weeks ago
1
[FEATURE] Remove unused data fields in summary results file
#30
molly-hetheringtonrauth
opened
3 weeks ago
0
[FEATURE] Version capture consistency across workflows
#29
molly-hetheringtonrauth
opened
1 month ago
2
merge develop into main
#28
molly-hetheringtonrauth
closed
1 month ago
0
Merge develop into main
#27
arianna-smith
closed
1 month ago
0
Fix bug with samples not in metadata
#26
arianna-smith
closed
1 month ago
1
[BUG] Novel mutations not erroring out in correct place
#25
arianna-smith
closed
1 month ago
0
[FEATURE] Create consistency between clinical and wwt mutation tracking
#24
molly-hetheringtonrauth
opened
2 months ago
0
[FEATURE] Deprecate nextclade_json_paser.py and use VCF files for Mutations Tracking
#23
molly-hetheringtonrauth
opened
2 months ago
0
[REQUEST] Rename WDL tasks to be more specific, standardized, or otherwise improved
#22
danpolanco
opened
2 months ago
3
[REQUEST] Update Freyja to 1.5.0
#21
arianna-smith
opened
2 months ago
1
Wip cdc variant url
#20
molly-hetheringtonrauth
closed
1 month ago
4
Novel mutations - ORF1ab, other updates
#19
arianna-smith
closed
3 months ago
0
[REQUEST] Update to Nextclade v3
#18
molly-hetheringtonrauth
opened
3 months ago
1
Medaka, read scrubbing, and version capture for v2.2.0 release
#17
sam-baird
closed
3 months ago
0
No transfer
#16
laura-bankers
closed
3 months ago
0
update "no-transfer" branch of wastewater variant calling
#15
laura-bankers
closed
3 months ago
0
Update novel mutations script to handle HSNs and new metadata columns
#14
arianna-smith
closed
3 months ago
0
[REQUEST] Update Aggregate Lineages to use CDC grouping URL
#13
molly-hetheringtonrauth
opened
4 months ago
0
Medaka updates for new 10.4.1 grid chemistry
#12
arianna-smith
closed
3 months ago
1
[REQUEST] Right size obvious tasks to alleviate resource exhaustion from CPU quota
#10
danpolanco
opened
5 months ago
0
Hardcode Nextclade version 2.14.0 until we can refactor to accommodate version 3
#9
danpolanco
closed
5 months ago
0
Fix/nextclade/hardcode v2
#8
danpolanco
closed
5 months ago
0
Hardcode v2 while we transition to v3 which solves --reference flag error and more
#7
danpolanco
closed
5 months ago
5
Add logging, simplify code, add docstrings, and check via pylint
#6
danpolanco
closed
2 months ago
2
Consolidate version capture tasks and scripts
#5
sam-baird
closed
3 months ago
2
Novel mutations
#4
arianna-smith
closed
6 months ago
0
Hardcode container versions
#3
arianna-smith
closed
7 months ago
0
Hardcode artic-ncov2019 version to 1.3.0
#2
arianna-smith
closed
7 months ago
0
Add QC metrics and improve efficiency in ONT assembly, lineage, and transfer WDLs
#1
sam-baird
closed
1 year ago
0