Code

Add CCHFV to loculus#1920

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anna-parker merged 81 commits intomainloculus-project/loculus:mainfrom ccfvloculus-project/loculus:ccfvCopy head branch name to clipboardJun 6, 2024

+1,224-341

Commits

Commits on May 22, 2024

• Add ccfv to yaml

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• Fix ingest for single segment case

  anna-parker

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• Fix: values.yaml - nucleotideSequences need to be a list in prepro configs and a dict in referencegenome configs.

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• Add correct genome annotations from NCBI

  anna-parker

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• Update configs to use githubusercontent for nextclade_datasets.

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• Use new dataset link

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• Fix preprocessing issues after default values.yaml changes.

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• Add segmented as a config param

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Commits on May 23, 2024

• Join segments based on isolate name.

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  49ff8e2

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• Fix some prepro issues

  anna-parker

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  1d9df16

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• Add default config changes

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• Update silo configs

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• Remove preprocessing temp results file.

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• Fix cchfv table columns as metdata has now been renamed.

  anna-parker

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• Fix author_affiliations

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• Merge branch 'main' into ccfv

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• Merge branch 'ccfv' of github.com:loculus-project/loculus into ccfv

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• Fix merge issues with instanceName.

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• Merge branch 'main' into ccfv

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• Fix prepare_metdata bug.

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  1d915a1

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• Merge branch 'ccfv' of github.com:loculus-project/loculus into ccfv

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• Add back missing website metadata.

  anna-parker

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• Fix author list sorting, fix displayName.

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Commits on May 24, 2024

• Fix values.yaml

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Commits on May 25, 2024

• Fix reingest.

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• Add segmented to ingest configs and make use in scripts consistent.

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• Update README.

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  60f5992

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• Fix little ingest bug

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Commits on May 27, 2024

• Refactor ingest to make steps clearer.

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• Fix webpage bug.

  anna-parker

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  31d1af1

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• Small prepro fixes

  anna-parker

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• Remove unnecessary files from gitignore

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Commits on May 28, 2024

• Merge branch 'main' into ccfv

  anna-parker

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• Small fixes

  anna-parker

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  38778f3

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• Merge branch 'ccfv' of github.com:loculus-project/loculus into ccfv

  anna-parker

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  80c52de

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• Clean up preprocessing

  anna-parker

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• add args

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• Use links to sequences instead of full sequences in values.yaml.

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  f535691

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• Merge branch 'main' into ccfv

  anna-parker

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  3cbbcc7

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• Fix little bug

  anna-parker

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  498a88d

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• Merge branch 'ccfv' of github.com:loculus-project/loculus into ccfv

  anna-parker

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  3e1c6e0

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• Fix length bug

  anna-parker

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  8b85432

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• Merge branch 'main' into ccfv

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• Merge branch 'ccfv' of github.com:loculus-project/loculus into ccfv

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  aacad98

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• Fix merge bug

  anna-parker

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  4b48c46

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• Make check stricter

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• Update docs

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Commits on May 31, 2024

• Merge remote-tracking branch 'origin/main' into ccfv

  anna-parker

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• Merge branch 'main' into ccfv

  anna-parker

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  eaba61f

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• Fix prepro bug introduced by merge

  anna-parker

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  b16026e

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• Merge branch 'ccfv' of github.com:loculus-project/loculus into ccfv

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  aab29a1

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• Remove ncbi_length from defaults - this was removed from values.yaml on main and is breaking ingest.

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• Update READMEs with suggestions.

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Commits on Jun 1, 2024

• Resolve some issues

  anna-parker

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Commits on Jun 2, 2024

• Change segmented to per_segment.

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Commits on Jun 3, 2024

• Remove the requirement for adding segmented:True to the config.yaml

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  28c9402

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• Fix backend bug

  anna-parker

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• Fix bug

  anna-parker

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• Second try to fix bug

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Commits on Jun 4, 2024

• Merge branch 'main' into ccfv

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Commits on Jun 6, 2024

• Add dag for segmented

  

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• Simplify segmentation inference

  

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• Remove unnecessary/confusing functions

  

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• Simplify extraction script, DRYer

  

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• Reorder to never have rules do forward references

  

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• Remove unused function

  

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• Keep top level dir clean by moving images to folder

  

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• Review segment parsing script

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• Switch default log level to INFO, debug is very verbose and there's no level lower than DEBUG

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• Log a few important lines at INFO, not everything at debug only

  

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• Avoid a very broad try/except block, if necessary, use in more localized manner

  

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• Mention all config in params: blocks, so snakemake can rerun rule on change

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• Use input.script consistently (the advantage of using the script as input is that this way snakemake will automatically rerun the rule when the script has been changed during development

  

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• All config files to be used by Python MUST use snake case, not camel case

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• Fix ruff lints and unnecessary indentations

  

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• Update documentation of group_segments

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• Fix issues raised in get_segment_details

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• Fix weird error I introduced when merging changes

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• Go back to old regex as this catches more cases.

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• Update ingest config file

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• Merge branch 'main' into ccfv

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