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Metadata output update

Gervaise Henry requested to merge new.qc.out into develop

Cumulative update focused on metadata output:

  • Add read length: both submitter entered and inferred (median length)
  • Add calculated read counts: both raw and assigned
  • Add median TIN
  • Output multiqc json (for future use)
  • Convert gene symbols to Entrez ID: for data-hub convenience (use version specific metadata - added to references)
  • Create bash script to initiate parallel replicate runs from study RID
  • Change consistence tests for assigned reads exact match to being within +/- 1/100,000 of expected

PR checklist

  • This comment contains a description of changes (with reason)
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated
  • Replace dag.png with the most recent CI pipleine integrated_pe artifact
  • CHANGELOG.md is updated
  • README.md is updated
  • LICENSE.md is updated with new contributors
  • Docker images moved to production release and changed in pipeline
  • Docker images used in the CI unit tests match those used in pipeline

/cc @ghenry @venkat.malladi

Edited by Gervaise Henry

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