CDPHE-bioinformatics/CDPHE-SARS-CoV-2

Issues

• [FEATURE REQUEST] Add depth and frequency to novel mutations

  #85 opened 4 days ago
  0

• [BUG] Error in `novel_mutations.py` when there are no new mutations, error with null `gff_feature`

  #81 opened 3 days ago
  1

• [Feature] Output sample level version capture file for sample level wf

  #80 opened 19 days ago
  0

• [BUG] Inconsistent scrubbed fastq folder names

  #77 opened 2 months ago
  1

• [REQUEST] Use BED file as input to Medaka for primer trimming

  #75 opened a month ago
  2

• [REQUIREMENT] Update Medaka for basecall model change

  #74 opened 2 months ago
  0

• [BUG/REQUEST] Update Artic to 1.5.2 for variant calling improvement and minor bug fix

  #71 opened a month ago
  1

• [REQUEST] Do not overwrite existing files by default

  #68 opened 2 months ago
  2

• [BUG] Error in lineage calling when there are no variants to output

  #64 opened 3 months ago
  0

• [BUG] CDC groupings dataset has bad data (i.e. NA lineage)

  #61 opened 3 months ago
  1

• [BUG] Broken code introduced in auto version update

  #60 opened 3 months ago
  0

• [BUG] Auto version path needs to be incorporated into WDL

  #57 opened 3 months ago
  0

• [REQUEST] Auto version should push back to develop

  #49 opened 3 months ago
  1

• [REQUEST] Auto version workflow using GitHub Action

  #42 opened 3 months ago
  4

• [REQUEST] samtools depth -aJ

  #41 opened 3 months ago
  1

• Switch from medaka to dorado

  #40 opened a month ago
  1

• [FEATURE] S gene coverage

  #39 opened 3 months ago
  2

• [REQUEST] Change sample-level workflows to set level and call downstream workflows as subworkflows

  #38 opened 4 months ago
  1

• [REQUEST] Use dynamic or customizable memory and disk size

  #37 opened 4 months ago
  1

• [REQUEST] Version Capture Files for Sample Level Workflows

  #36 opened 4 months ago
  2

• [REQUEST] Add version number as subfolder of terra_outputs

  #35 opened 5 months ago
  0

• [BUG] Awk command adding extra whitespace to mutations files

  #32 opened 4 months ago
  0

• Invalid escape sequence in newer versions of python

  #31 opened 7 months ago
  1

• [FEATURE] Remove unused data fields in summary results file

  #30 opened 7 months ago
  1

• [FEATURE] Version capture consistency across workflows

  #29 opened 7 months ago
  3

• [BUG] Novel mutations not erroring out in correct place

  #25 opened 7 months ago
  0

• [FEATURE] Create consistency between clinical and wwt mutation tracking

  #24 opened 4 months ago
  1

• [FEATURE] Deprecate nextclade_json_paser.py and use VCF files for Mutations Tracking

  #23 opened 4 months ago
  1

• Rename WDL tasks to be more specific, standardized, or otherwise improved

  #22 opened 8 months ago
  3

• [REQUEST] Update Freyja to 1.5.1

  #21 opened 2 months ago
  4

• Update to Nextclade v3 and deprecate parser

  #18 opened 9 months ago
  2

• update "no-transfer" branch of wastewater variant calling

  #15 opened 10 months ago
  0

• Update novel mutations script to handle HSNs and new metadata columns

  #14 opened 9 months ago
  0

• [REQUEST] Update Aggregate Lineages to use CDC grouping URL

  #13 opened 2 months ago
  0

• Right size obvious tasks to alleviate resource exhaustion from CPU quota

  #10 opened a year ago
  1

• Hardcode v2 while we transition to v3 which solves --reference flag error and more

  #7 opened a year ago
  5