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PacificBiosciences / pb-human-wgs-workflow-wdl

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Update the trio to deal with some additional options #55

Closed vsmalladi closed 1 year ago

vsmalladi commented 2 years ago

Addressed the following:

  1. a singleton case
  2. 2 or more probands (kids) without any parents,
  3. single or both parents only case or one or more probands (kids) with single or both parents.
  4. Parents do not have to be of unaffecteds, they could be of affecteds in many cases
  5. Probands (children) do not have to be of affecteds, they could be of unaffecteds in some case.
ducatiMonster916 commented 1 year ago

We just met for a code review- the PR should satisfy all edge cases listed. Approved for merging & testing

williamrowell commented 1 year ago

@byoo @vsmalladi @ducatiMonster916 Merged.

byoo commented 1 year ago

@vsmalladi @ducatiMonster916, I couldn't validate the pipeline. Could you check?

Failed to import 'https://raw.githubusercontent.com/PacificBiosciences/pb-human-wgs-workflow-wdl/main/workflows/smrtcells/smrtcells.trial.wdl' (reason 1 of 1): Failed to import 'https://raw.githubusercontent.com/PacificBiosciences/pb-human-wgs-workflow-wdl/main/workflows/smrtcells/smrtcells.person.wdl' (reason 1 of 1): Failed to process workflow definition 'smrtcells_person' (reason 1 of 1): Failed to process declaration 'Array[String?] parents_names = sample.parents' (reason 1 of 1): Cannot coerce expression of type 'Array[String]?' to 'Array[String?]' Failed to import 'https://raw.githubusercontent.com/PacificBiosciences/pb-human-wgs-workflow-wdl/main/workflows/sample/sample_trio.trial.wdl' (reason 1 of 2): Failed to import 'https://raw.githubusercontent.com/PacificBiosciences/pb-human-wgs-workflow-wdl/main/workflows/sample/tasks/hifiasm_trio.wdl' (reason 1 of 2): Failed to process workflow definition 'hifiasm_trio' (reason 1 of 2): Failed to process 'call hifiasm_trio_assemble' (reason 1 of 2): Failed to supply input parent2_yak = parent2_yak (reason 1 of 1): Cannot coerce expression of type 'Array[File?]' to 'File' Failed to import 'https://raw.githubusercontent.com/PacificBiosciences/pb-human-wgs-workflow-wdl/main/workflows/sample/sample_trio.trial.wdl' (reason 2 of 2): Failed to import 'https://raw.githubusercontent.com/PacificBiosciences/pb-human-wgs-workflow-wdl/main/workflows/sample/tasks/hifiasm_trio.wdl' (reason 2 of 2): Failed to process workflow definition 'hifiasm_trio' (reason 2 of 2): Failed to process 'call hifiasm_trio_assemble' (reason 2 of 2): Failed to supply input parent1_yak = parent1_yak (reason 1 of 1): Cannot coerce expression of type 'Array[File?]' to 'File'