Release v64.5.15

Patch orders pagination (#3981) (patch)

Fixed

• Pagination is applied even when workflow is not set

Release v64.5.14

Set parameters in params file, and not config (#3965) | major

• Rename workflow_path to workflow_bin_path to make clearer that we are talking about the codebase of the workflow
• Renamed config_resources into resources, config_platform into platform
• Split config_params into params and config
• Building parameters with config_case now has a part with cg-built(or fetched) parameters that is added to the parameter file from servers. Placeholders are used and replaced by the value extracted from the same parameter dictionary, to avoid typos/repeats
• Use target_bed_file instead of target_bed because target_bed needs the path to the reference directory that is defined in servers -> target_bed_file is the filename and target_bed in params uses that with the reference path to build the full file path
• Removed unused is_params_appended_to_nextflow_config function
• Add references are specified in params files from servers and don't need to be read-in and handled by cg

Release v64.5.13

feat(analysisType): Remove rna (#3973)

Changed

• Remove unused AnalysisType rna

Release v64.5.12

Refactor prep category (#3961)

Changed

• Rename PrpeCategory to SeqLibPrepCategory
• Move the class to sequencing.py under constants
• Removed implicit import from constant/init.py
• DRY: Removed SequencingMethod as it is dictated by SeqLibPrepCategory

Release v64.5.11

refactor(decompose sample file formatter) (#3960) (patch)

Description

refactoring of the sample file formatters

Release v64.5.10

feat(gunicorn): Add config (#3894)

Changed

• Add Gunicorn config
• Update werkzeug

Release v64.5.9

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

Release v64.5.8

feat(refactor): (#3957)

Changed

• Refactor get-families-with-samples

Release v64.5.7

feat(refactor): get_families_with_analyses (#3928)

Change

• Refactor get_families_with_analyses

Release v64.5.6

Refactor get cases for analysis (#3926)

Changed

• Refactor cases_to_analyse