pull from devel to master to create release 99.0.0 #803
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This generator was writted for MiSeq instrument format. Will have to be extended to include NovaSeqX format. This pull request, while not changing the current functionality, opens a way to extend the generator to other formats.
XML driver for st::api::lims was removed some time ago... The build method the 'lims' attribute is simplified since only the ml_warehouse driver is now used.
Removed provisions for XML driver in samplesheet generation.
Most likely, this file was never needed and ended up in the repo by mistake.
Removed unused test data.
Added tests for the content of generated samplesheets to drive DRAGEN analysis on-board.
Generalised auto-generator for samplesheets.
Tested the content of NovaSeqX samplesheet.
Commented out code deleted. Attributes and methods are ordered more logically. Some private accesors are converted to public. Documentation improved. Added index_read_length and read_length attributes so that these values can be set by the caller.
Improved samplesheet generation for NovaSeqX.
Created a parent class for two existing samplesheet generators. Moved common methods to this class. Through this inheritance the NovaSeqX samplesheet generator gets a standard method for setting a configurable path for a samplesheet.
An option to read the value from the configuration file is not used.
Ability to set a path for NovaSeqX samplesheet
Added a test to test the correctness of passing the option to teh samplesheet generator.
The object used the ml_warehouse driver. This tests demonstrates that the children of such object are created correctly, their sample properties can be accessed.
Tests moved from t/40-st-lims.t to t/40-st-lims-merge.t since similar functionality for creating a lane object is tested in t/40-st-lims-merge.t t/40-st-lims.t is now left to test methods for retrieving LIMS data using the samplesheet driver.
... to use copy_init_args method instead of _driver_arguments method mostly in order to be consistent. Since this method is called in the run-level object, it does not suffer from the same problems as other methods, which had to be updated in this pr. All new tests for this commit passed without changing the code.
Was needed when we used the xml driver. No current lims driver is using this argument. Existing production code does not pass batch_id to st::api::lims constructor. st::api::lims documentation updated.
The old samplesheet generator had this ability. Rearranged the code so that the samplesheet generator for NovaSeqX also has this ability, which simplifies the code in the samplesheet daemon. NovaSeqX samplesheet generator retains ability to generate a samplesheet when neither id_run nor the run db record is set via the constructor.
Correctly propagate driver details for mlwh driver
Removed st::api::lims batch_id constructor arg.
Daemon4novaseqx samplesheet
Recorded recent changes
Update emails for status change
Updated branch for dependencies on push.
prep release 99.0.0
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