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Clone case#52

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sbreiff wants to merge 18 commits intomasterfrom
clone_case
Open

Clone case#52
sbreiff wants to merge 18 commits intomasterfrom
clone_case

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@sbreiff sbreiff commented Sep 9, 2021

This PR adds a check and action for cloning cases. In this current version, a new meta-wfr is associated with the cloned case(s) but it will be newly created and start from scratch - i.e. we won't be able to specify a particular step to start from and clone the old meta-wfr. We intend to implement that ability in a later version after this first version is in.

get_metadata_for_cases_to_clone check:

  • needs version and accessions kwargs
  • looks up uuid of the metawf that should be attached to the cloned case
  • case ignored if no meta-wfr already on it
  • case ignored if meta-wfr on it is associated with a meta-wf that doesn't have a version specified in the kwarg (e.g., if a case has a mwfr from WGS trio v24, and v25 is the latest version of WGS trio metawf, but v26 was put in the kwarg, then this case will get ignored)
  • case ignored if meta-wfr on it is already the version specified in the kwarg

clone_cases action:

  • clones cases (if its a group analysis, will also clone non-proband cases)
  • clones samples, creates new sample_processing
  • family, individual, fastq items not duplicated but are associated properly
  • new meta-wfr is created with specified version but will start from scratch

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