Sample sheets for single-sample lanes failing validation

[diitaz93]

Filled together with @Karl-Svard

As a production user who encounters a sample sheet of a flow cell with one sample per lane and that has no index in its samples, I want the sample sheet not to fail validation, So that the flow cell can be automatically demultiplexed and post-processed.

Acceptance Criteria

• [x] The change should only happen when there is one sample per lane that has no indexes
• [x] The sample sheet has to be accepted by DRAGEN in the demultiplex
• [x] The sample sheet has to allow post-processing ...

Notes

This has happened twice in the last weeks, most likely from flow cells whose sample sheets were regenerated from Bcl2fastq to BCLConvert. One of the flow cells in H3YVCALXX

Clarification

The validation cg performs on a sample sheet disallows samples with no indices even though they are permitted by the demux software.

Also the samplesheet generated by cg is not accepted by the validation on dragen.

Implementation plan

• [ ] Fix generation/validation of OverrideCycles for the flow cells with only one sample per lane and samples without indices
• [ ] Remove the barcode mismatch columns from this flow cell
• [ ] Update tests with this new flow cell (add this case to canonical flow cells)

[diitaz93]

Technical refinement

1. Modify the OverrideCycles validator in cg/apps/demultiplex/sample_sheet/override_cycles_validator.py so that it parses correctly null indexes

[diitaz93]

Affected FC: 161206_ST-E00201_0170_BH57JWALXX

[diitaz93]

Happened again to flow cell 160401_ST-E00266_0079_BHK3YTCCXX, bumping the priority of this

[diitaz93]

@Karl-Svard found the root cause of this issue in LIMS and patched it for the affected indexes. Re-open and inform KSV if this happens again