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@clingen-sthlm clingen-sthlm released this 25 Nov 06:36
· 154 commits to master since this release
v64.5.9
429f7d9

patch - Concatenate Microbial fastq files (#3958)(patch)

Description

Addresses Clinical-Genomics/bug-reports#17
The Microbial fastq orders currently behave in the backend as a normal fastq order, while in reality, they should have a hybrid functionality between Microsalt and fastq. This is, the raw data fastq files should be concatenated for a sample (the replicates in multiple lanes) as it is done in Microsalt, but no analysis should start, as in fastq orders.

This PR overwrites the Workflow of Microbial-fastq cases from Workflow.RAW_DATA to Workflow.MICROSALT just for the delivery service.

Added

  • Static method _convert_workflow in DeliveryServiceFactory that patches the workflow of microbial fastq cases as Microsalt
  • Unit test for new function

Changed

  • The parameters of the public function build_delivery_service from DeliveryServiceFactory to receive case and delivery_type instead of Workflow and delivery_type

Fixed

  • All calls to build_delivery_service with the new parameters
  • Tests for build_delivery_service
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