Releases: Clinical-Genomics/cg
Release v38.0.1
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
anddemux_post_processing
modules
Release v38.0.0
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
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
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
andget_hamming_distance_index_1
(and its test functions) incg/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
incg/apps/demultiplex/sample_sheet/index.py
and replaced it with two functions:adapt_indexes_for_sample
andadapt_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
fix(RML OF) Renamed new indexset (#2207)(patch)
Fixed
- Renamed Illumina Nextera XT Dual to Nextera XT Dual
Release v37.0.26
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
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
Release v37.0.23
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.