nextstrain/ncov

Issues

• Migrate to Nextclade v3

  #1157 opened 2 months ago by joverlee521
  0

• Improve / standardize the way that we pass through default parameters and build-specific parameters

  #1131 opened 4 months ago by trvrb
  6

• Highlight currently circulating viruses

  #1143 opened 4 months ago by genehack
  2

• Augur 26 breaks 21L workflow due to duplicate sequences erroring in augur filter

  #1155 opened 2 months ago by corneliusroemer
  2

• gisaid/21L builds failing on duplicate sequences

  #1153 opened 2 months ago by victorlin
  2

• Use weighted sampling

  #1141 opened 2 months ago by victorlin
  0

• Remove redundancy in config file values

  #1144 opened 3 months ago by victorlin
  4

• CI failing with Augur 25.3.0

  #1146 opened 3 months ago by victorlin
  1

• Define workflow dependencies

  #1118 opened 5 months ago by victorlin
  0

• Fix broken links in docs

  #1133 opened 4 months ago by genehack
  0

• Fix czbiohub covidtracker community build link

  #1136 opened 4 months ago by genehack
  0

• Fix broken template_narritave link

  #1135 opened 4 months ago by genehack
  0

• CI: docs build failing

  #1126 opened 4 months ago by victorlin
  5

• Workflow fails on Snakemake 8.x

  #1114 opened 5 months ago by ggonnella
  4

• representation of a nuc conversion do not point a conversion on the genome

  #1107 opened 7 months ago by huzuner
  4

• Port builds to `pathogen-repo-build`

  #1113 opened 5 months ago by joverlee521
  1

• Entropy calculation

  #1124 opened 5 months ago by rabiakasikci
  1

• Remove `nextstrain_profiles/nextstrain-country`

  #1120 opened 5 months ago by joverlee521
  5

• Rename `master` to `main`

  #1116 opened 6 months ago by genehack
  0

• [Question] How does Nextstrain handle recombinant SARS-CoV-2 lineages in phylogenetic analysis?

  #1112 opened 6 months ago by llk578496
  2

• /bin/bash: nextclade2: command not found

  #1110 opened 6 months ago by llk578496
  4

• Port CI to `pathogen-repo-ci` GH Action workflow

  #1109 opened 6 months ago by genehack
  1

• FileNotFoundError: [Errno 2] No such file or directory: 'ncov-tutorial/example-data.yaml'

  #1108 opened 7 months ago by kiranpatil222
  2

• Dataset JSONs are not minified

  #1098 opened 10 months ago by tsibley
  0

• possible broken wf with nextclade update

  #1093 opened 10 months ago by arodzh-sudo
  1

• Missing input files for rule align:

  #1092 opened 10 months ago by liamxg
  1

• Add 16 NSPs

  #1081 opened a year ago by jameshadfield
  0

• botocore/boto3 SSL certificate error when using self-signed certificates

  #1055 opened 2 years ago by jacaravas
  1

• ValueError: Fasta file appears to have sequences of different lengths!

  #1079 opened a year ago by tibitoy
  4

• Proposal: elevate XBB.1.9 as 23C

  #1073 opened a year ago by NkRMnZr
  6

• Aliased & Unaliased Search Options for 21L

  #1076 opened a year ago by ryhisner
  2

• Deduplication metadata fails

  #1049 opened 2 years ago by mwelkers
  6

• tests/different-inputs.t is outdated and unused

  #1061 opened 2 years ago by victorlin
  1

• Why use unaligned sequences as "aligned" input instead of the actually aligned sequences?

  #1054 opened 2 years ago by tsibley
  5

• can't install to native

  #1053 opened 2 years ago by shujiuli
  4

• Query Contains a Column That Does Not Exist in Metadata.

  #1052 opened 2 years ago by Samiah-Kanwar
  5

• dev: Document example accepted docker image formats for action

  #1051 opened 2 years ago by corneliusroemer
  2

• Proposal: elevate XBB.1.5 as 22G

  #1040 opened 2 years ago by AnonymousUserUse
  2

• download the Frequencies (colored by Clade )

  #1042 opened 2 years ago by timktsang
  1

• PermissionError: [Errno 13] Permission denied: '.snakemake'

  #1041 opened 2 years ago by spencel
  3

• Proposal: elevate BN.1 as 22G

  #1031 opened 2 years ago by AnonymousUserUse
  2

• after skip_diagnostics: true modification. next strain fails

  #1035 opened 2 years ago by Valentin-Bio-zz
  3

• feat: WDL overhaul for Dockstore and Terra

  #1005 opened 2 years ago by j23414
  0

• ENH: Make trial build URLs real, not require replacement

  #1019 opened 2 years ago by corneliusroemer
  1

• URL preview from rebuild-gisaid.yml output does not work

  #990 opened 2 years ago by victorlin
  2

• Discussion: Do we still need the `snp_clusters` param for `diagnostics` rule?

  #1017 opened 2 years ago by joverlee521
  3

• ENH: Simple reversion coloring to allow inspection of interesting/problematic parts of tree

  #1015 opened 2 years ago by corneliusroemer
  0

• ENH: Reconstruct Nextclade Pango Lineage on internal nodes

  #1011 opened 2 years ago by corneliusroemer
  0

• data download for "all-time" Europe is empty

  #989 opened 2 years ago by eltrompetero
  9

• ENH: Add S1 mutations, reversion count and other branch colorings

  #985 opened 2 years ago by corneliusroemer
  0