Release v38.1.8

Add integration test for post processing of flow cell demultiplexed with bcl2fastq (#2235)

Fixed

• Add integration test for post processing of flow cell demultiplexed with bcl2fastq

Release v38.1.7

change(Balsamic): Automatic start of normal only analyses (#2214)

Changed

• Normal only balsamic analysis starting automatically

Removed

• force-normal flag

Release v38.1.6

added novaseqx support flow cell model (#2239) (patch)

Description

Change the column type of the sequencer_type column in the FlowCell model in statusDB to accept novaseqx.

Release v38.1.5

feat(Balsamic): upload of SVs to Scout for UMI cases (#2232)

Added:

• Upload of SVs to Scout for UMI cases

Release v38.1.4

add(novaseqx demux post processing) (#2227) (patch)

This PR addresses the issue outlined in #2168.

The changes in the bcl_convert.py file include:

Removed the import statement for xml.etree.ElementTree as it is not used in the code.
Replaced the hardcoded file paths with constants for the following files: DEMUX_METRICS_FILE_PATH, QUALITY_METRICS_FILE_PATH, ADAPTER_METRICS_FILE_PATH, and SAMPLE_SHEET_FILE_PATH. The constants are now defined as file names: DEMUX_METRICS_FILE_NAME, QUALITY_METRICS_FILE_NAME, ADAPTER_METRICS_FILE_NAME, and SAMPLE_SHEET_FILE_NAME.
Added a new import statement for the get_file_in_directory function from cg.utils.files.
Modified the initialization of self.quality_metrics_path, self.demux_metrics_path, self.adapter_metrics_path, and self.sample_sheet_path to use the get_file_in_directory function to get the corresponding file paths based on the directory specified.
Updated the get_nr_of_header_lines_in_sample_sheet method to accept the sample_sheet_path as a parameter instead of using self.sample_sheet_path directly.
Updated the parse_sample_sheet_file method to accept the sample_sheet_path as a parameter instead of using self.sample_sheet_path directly.
Modified the self.sample_sheet assignment to use the parse_sample_sheet_file method with the self.sample_sheet_path as an argument.
In the bcl_convert_metrics.py file, the constants DEMUX_METRICS_FILE_PATH, QUALITY_METRICS_FILE_PATH, ADAPTER_METRICS_FILE_PATH, and SAMPLE_SHEET_FILE_PATH have been replaced with DEMUX_METRICS_FILE_NAME, QUALITY_METRICS_FILE_NAME, ADAPTER_METRICS_FILE_NAME, and SAMPLE_SHEET_FILE_NAME, respectively. These constants now hold the file names instead of the file paths.

In the flow_cell.py file, the sequencer_type property has been modified to return the value of sequencer_types[self.machine_name].value instead of sequencer_types[self.machine_name].

A new file files.py has been added under cg/utils directory, which contains a get_file_in_directory function. This function is used to get a file in a directory and its subdirectories based on the specified file name.

In the conftest.py file under tests/utils, two new fixtures have been added: some_file and nested_directory_with_file. some_file returns a string representing a file name, and nested_directory_with_file returns a Path object representing a directory with a nested subdirectory and a file.

A new file test_files.py has been added under tests/utils, which contains a test for the get_file_in_directory function. The test verifies that the function returns the correct file path when given a directory and a file name.

Release v38.1.3

Add integration test for post processing of flow cell demultiplexed with Bcl Convert (#2224)(patch)

Fixed

• Add integration test for post processing of bclconvert demultiplexed flow cell

Release v38.1.2

#2056: Move fixtures to root conftest (#2230)(patch)

Fixed

• Remove direct imports of demux fixtures by moving fixtures into root conftest

Release v38.1.1

Remove parsing of unused information in BclConvertMetricsParser (#2229)(patch)

Fixed

• Remove parsing of unused information from RunInfo.xml in sequencing metrics parser

v38.1.0

Added

• Field to Customer table called "data_archive_location" with type str(32).
• Alembic revision to reflect the change.

Release v38.0.2

Refactor RNA DNA case map to data class (#2210) (patch)

Changed

• The nested dictionary is replaced with a data class containing an rna_sample_id, a dna_sample_name and a list of DNA cases; dna_cases.
• Tests reworked to test the new functionality.