Organise demultiplex tests and fixtures around only 7 flow cell cases #2842
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diitaz93
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This is the first step of #2842. Refactor the fixtures returning lists of `FlowCellSample` to only use elements from the 7 canonical flow cells in demultiplexing ### Added - Raw sample file `tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/HLYWYDSXX_bcl2fastq_raw.json` with anonymised names and projects ### Changed - Renamed `novaseq_6000_pre_1_5_kits_lims_samples` and `novaseq_6000_post_1_5_kits_lims_samples` to explicitly include the bcl converter in their name ### Fixed - Removed fixture `lims_novaseq_6000_bcl2fastq_samples`, replaced usages with `novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples`. - Removed fixture `lims_novaseq_bcl_convert_samples`, replaced usages with `novaseq_x_lims_samples` - Removed paths to lims sample files that were used only once. Instantiated Path in the fixture where they were used instead.
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diitaz93
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…)(patch) ## Description Part of #2842. First attempt to leave only fixtures of only 7 flow cells. Removed and renamed flow cell fixtures and their files. PR was growing too much so decided to stop this one here and continue in another PR. ### Added - Directory `flow_cells_broken` to distinguish the files from working flow cells from flow cells missing files (required by some tests) ### Changed - Renamed several fixtures ### Fixed - Removed fixtures and files for flow cells 180522_A00689_0200_BHLCKNCCXY and 170407_A00689_0209_BHHKVCALXX
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@diitaz93 Done? |
@henrikstranneheim Not yet, there is still a lot of debris from old fixtures that unfortunately are still used in some tests. A further cleaning is needed. I want to do this this summer if I have time but this is low prio |
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Very low prio, not keeping as an issue |
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Description
In the context of demultiplexing, I have identified 7 different Illumina flow cell cases that share many characteristics:
The idea is that the demultiplexing test suite is designed around these 7 cases. For this, I chose one example from each group and added the flow cell directory data to the folder
tests/fixtures/apps/demultiplexing/flow_cellsin #2736. However, many tests and fixtures still use elements spread around the test directory from different flow cells in a disorganised way.Suggested solution
With the help of fixture plugins introduced in #2816, create an organised set of fixtures that replaces old ones pointing to inconsistent flow cells with correct fixtures pointing to one of the 7 case flow cells.
PRs:
Pending tasks:
CorrectSampleSheet.csvas all sample sheets in the flow cell folders should be correct, ill-shaped sample sheets should be in thebroken_flow_cellsfixture directoryThis can be closed when
The demultiplexing testing suite is designed around the 7 flow cell cases.
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