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Releases: Clinical-Genomics/cg

Release v38.0.1

05 Jul 13:15
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Only store sample fastqs passing q30 in Housekeeper (#2201)(patch)

  • q30 check before storing sample fastq paths in housekeeper
  • Extract utils methods from DemuxPostProcessingAPI to a separate utils module
  • Extract validation methods from DemuxPostProcessingAPI to a separate validation module
  • Renaming of methods to accurately reflect what is done in the method body
  • Unit tests for the validation, utils and demux_post_processing modules

Release v38.0.0

04 Jul 14:39
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enhance(usability delete flow cell command) (#2204) (major)

Description

Refactoring of delete-flow-cell command.

Changes to cg demultiplex delete-flow-cell command:

The cli command now takes the flow cell name (e.q. HX41JJXR) instead of the flow cell directory (XXXX_XXXX_HX41JJXR) as input.

Release v37.2.0

04 Jul 10:27
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fix(RNAFUSION orders) Add validation for one sample per case (#2209)(minor)

Added

  • Validation for RNAFUSION orders to only allow one sample per case

Release v37.1.0

03 Jul 13:59
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feat (SampleSheet) add barcode mismatch based on hamming distance (#2138)(minor)

Added

  • function cg/apps/demultiplex/sample_sheet/index.py: get_index_pair (and its test functions).
  • function cg/apps/demultiplex/sample_sheet/index.py: adapt_barcode_mismatch_values_for_sample (and its test functions) that adapts the barcode mismatch values of a sample.
  • functions get_hamming_distance_index_1 and get_hamming_distance_index_1 (and its test functions) in cg/apps/demultiplex/sample_sheet/index.py that calculate the hamming distance between two indices 1 and 2 respectively.
  • function cg/utils/utils.py:get_hamming_distance (and its test functions) that calculates the hamming distance between two general strings.
  • More unit tests for functions in cg/apps/demultiplex/sample_sheet/index.py
  • function cg/apps/demultiplex/sample_sheet/create.py:sample_sheet_creator_factory that defines the type of creator based on the sequencer.
  • function cg/apps/demultiplex/sample_sheet/sample_sheet_creator.py:process_samples_for_sample_sheet that deals with pre-processing samples before sample sheet generation

Changed

  • Removed function adapt_indexes in cg/apps/demultiplex/sample_sheet/index.py and replaced it with two functions: adapt_indexes_for_sample and adapt_samples.

Fixed

  • Called the function adapt_samples over all samples in a lane, not in all the flow cell. Iterate then over lanes.

Release v37.0.28

03 Jul 12:27
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fix(RML OF) Renamed new indexset (#2207)(patch)

Fixed

  • Renamed Illumina Nextera XT Dual to Nextera XT Dual

Release v37.0.26

03 Jul 06:38
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Fix update date in uploading MIPRNA (#2203)(patch)

Added

  • A return that avoids ùploaded_at` be updated for not uploaded samples

Changed

Fixed

  • Moved the self.update_uploaded_at(analysis) outside the if statement for scout delivery

Release v37.0.25

30 Jun 12:18
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Filter on q30 threshold for update of read count (#2199)(patch)

Fixed

  • Use q30 threshold when updating the sample read count

Release v37.0.24

30 Jun 08:52
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fix model import (#2200) (patch)

Description

part of #2097

Fixes a model import pointing to the wrong Version model used in a typehint.

Release v37.0.23

29 Jun 14:10
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add flow cell and sample links to table (#2198) (patch)

Description

Add clickable links that refer to the flow cell and samples to the sample sequencing metrics table in statusDB.

Release v37.0.22

29 Jun 13:19
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Change log messages to debug (#2196)(patch)

Fixed

  • Change some logging to debug mode