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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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Update to artic v1.5.3 (medaka to clair3)
#78
sam-baird
closed
6 days ago
0
[BUG] Inconsistent scrubbed fastq folder names
#77
arianna-smith
opened
2 weeks ago
1
Update Medaka for new basecall models and model auto-detect.
#76
sam-baird
closed
2 weeks ago
0
[REQUEST] Use BED file as input to Medaka for primer trimming
#75
sam-baird
closed
2 days ago
2
[REQUIREMENT] Update Medaka for basecall model change
#74
sam-baird
closed
2 weeks ago
0
Fix freyja 1.5.2 reversion issues
#73
arianna-smith
closed
3 weeks ago
0
Fix previous merge auto-version, change default version bump to patch
#72
arianna-smith
closed
3 weeks ago
0
[BUG/REQUEST] Update Artic to 1.5.2 for variant calling improvement and minor bug fix
#71
arianna-smith
closed
6 days ago
1
Patch level fix - Update Freyja to 1.5.2
#70
arianna-smith
closed
3 weeks ago
0
Update Freyja to 1.5.2
#69
arianna-smith
closed
3 weeks ago
0
[REQUEST] Do not overwrite existing files by default
#68
sam-baird
opened
3 weeks ago
2
Fix accidentally deleted line
#67
arianna-smith
closed
1 month ago
0
Patch level bug fixes for auto versioning, NAs, and nextclade empty file failure
#66
danpolanco
closed
1 month ago
0
Bug fix- lineage calling
#65
arianna-smith
closed
1 month ago
0
[BUG] Error in lineage calling when there are no variants to output
#64
arianna-smith
closed
1 month ago
0
More fixes for #61.
#63
danpolanco
closed
1 month ago
0
Fix error caused by bad NA in CDC lineage grouping dataset
#62
danpolanco
closed
1 month ago
0
[BUG] CDC groupings dataset has bad data (i.e. NA lineage)
#61
danpolanco
closed
1 month ago
1
[BUG] Broken code introduced in auto version update
#60
danpolanco
closed
1 month ago
0
Fix workflow version passing from period to dashes
#59
danpolanco
closed
1 month ago
0
Change to use workflow_version_path instead of relying on non-path version
#58
danpolanco
closed
1 month ago
0
[BUG] Auto version path needs to be incorporated into WDL
#57
danpolanco
closed
1 month ago
0
Remove whitespace around next version
#56
danpolanco
closed
1 month ago
0
Fix missing line for next version tag
#55
danpolanco
closed
1 month ago
0
Fix sed with correct output from dry run
#54
danpolanco
closed
1 month ago
0
Fix git config so it is after checkout
#53
danpolanco
closed
1 month ago
0
Move git config earlier in github action
#52
danpolanco
closed
1 month ago
0
Remove trailing redirect for workflow version
#51
danpolanco
closed
1 month ago
0
Push version bump to develop
#50
danpolanco
closed
1 month ago
0
[REQUEST] Auto version should push back to develop
#49
danpolanco
closed
1 month ago
1
Continue to debug github action
#48
danpolanco
closed
1 month ago
0
Continue to debug github action
#47
danpolanco
closed
1 month ago
0
Fix to use outputs instead of echo for sed search and fix typo in git…
#46
danpolanco
closed
1 month ago
0
Fix typo for version capture task auto version
#45
danpolanco
closed
1 month ago
0
Merge in auto versioning
#44
danpolanco
closed
1 month ago
0
[REQUEST] Add auto increment for workflow version following SemVer conventions.
#43
danpolanco
closed
1 month ago
0
[REQUEST] Auto version workflow using GitHub Action
#42
danpolanco
closed
1 month ago
4
[REQUEST] samtools depth -aJ
#41
molly-hetheringtonrauth
opened
2 months ago
1
Switch from medaka to dorado
#40
danpolanco
closed
1 week ago
1
[FEATURE] S gene coverage
#39
molly-hetheringtonrauth
opened
2 months ago
2
[REQUEST] Change sample-level workflows to set level and call downstream workflows as subworkflows
#38
arianna-smith
opened
2 months ago
1
[REQUEST] Use dynamic or customizable memory and disk size
#37
sam-baird
closed
2 months ago
1
[REQUEST] Version Capture Files for Sample Level Workflows
#36
molly-hetheringtonrauth
closed
2 months ago
2
[REQUEST] Add version number as subfolder of terra_outputs
#35
arianna-smith
opened
3 months ago
0
Merge develop into main
#34
arianna-smith
closed
4 months ago
1
Fix and update combined_mutations.tsv creation
#33
arianna-smith
closed
4 months ago
1
[BUG] Awk command adding extra whitespace to mutations files
#32
arianna-smith
closed
2 months ago
0
Invalid escape sequence in newer versions of python
#31
danpolanco
opened
5 months ago
1
[FEATURE] Remove unused data fields in summary results file
#30
molly-hetheringtonrauth
opened
5 months ago
1
[FEATURE] Version capture consistency across workflows
#29
molly-hetheringtonrauth
opened
6 months ago
2
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