CL pipeline failure

[Caroline-99]

[aleixpuigb]

We should only add the CL_agreed TRUE, otherwise we might encounter more CL label repetitions.

[hkir-dev]

In the HLCA source file there are two clusters annotated as bronchial goblet cell and CL_agreed TRUE (line 27 and 29), that seems to be the reason.

Is this a copy error made by me, should I keep only one of these?

Also, David mentioned:

If markers are going into CL there needs to be a single cluster per dataset + the CL mapping could differ from CxG.

[aleixpuigb]

One is a more specific term that is not CL agreed.

[hkir-dev]

Sorry, I couldn't understand the solution. Should I make the first one False?

index	cl_class	cl_label	Cell_type	Marker_set	Minimal_markers	Minimal_markers_label	Organ	...	CL_agreed
27	CL:1000312	bronchial goblet cell	Goblet (bronchial)	CLM:1000026	ensembl:ENSG00000197943|ensembl:ENSG00000174501	PLCG2|ANKRD36C	Lung	...	True
29	CL:1000312	bronchial goblet cell	Goblet (subsegmental)	CLM:1000028	ensembl:ENSG00000255823|ensembl:ENSG00000149021	MTRNR2L8|SCGB1A1	Lung	...	True

[aleixpuigb]

I think this is because the problem with the PR incorporating commits from a different branch. CLM:1000028 should have remained False.

[hkir-dev]

resolved by #13