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PacificBiosciences / pb-human-wgs-workflow-wdl

BSD 3-Clause Clear License
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Fix outstanding issues. #64

Closed vsmalladi closed 1 year ago

vsmalladi commented 1 year ago
  1. Sample-level pbsv run doesn't compress and index the output VCF Closes #62
  2. Use local copies of resources instead of dynamic download Closes #65
  3. pbsv_call fails when the provided referece has suffix of .fna instead of .fasta Closes #57
  4. yak runs once if used for multiple siblings . Closes #63
  5. Use ubam for hifiasm for now. Closes #67
  6. Clarify documentation to use URL + SAS token. Closes #58
vsmalladi commented 1 year ago

@williamrowell @ducatiMonster916 @byoo @cbi-star

All changes made ready for review.

williamrowell commented 1 year ago

Remove workflows/reference/tasks/.DS_Store.

vsmalladi commented 1 year ago

Remove workflows/reference/tasks/.DS_Store.

Fixed. And added .gitignore.

byoo commented 1 year ago

@vsmalladi, it doesn't validate using womtool version 73 that's used by CoA. Could you check?

Failed to import 'https://raw.githubusercontent.com/PacificBiosciences/pb-human-wgs-workflow-wdl/main/workflows/sample/sample_trio.trial.wdl' (reason 1 of 1): Failed to process workflow definition 'sample_trio' (reason 1 of 1): Failed to process declaration 'Array[Array[String]] affected_person_parents_names_n = select_first([affected_person_parents_names, [["None"]]])' (reason 1 of 1): Cannot coerce expression of type 'Array[Array[String]?]' to 'Array[Array[String]]'