No control over number of PCs in batch_correct_none

[wlason]

I have a complex study design with not all antibodies present in every sample (there are 24 in total).
I would like to run protein batch correction using harmony with 10 PCs, the number of PCs gets correctly parsed to harmony, but not to no correction workflow, resulting in an error.

ValueError: n_components=20 must be between 1 and min(n_samples, n_features)=19 with svd_solver='arpack'

panpipes/panpipes/python_scripts/batch_correct_none.py

Lines 96 to 99 in 0bc49a4

	if adata.var.shape[0] < n_pcs:
	L.info("You have less features than number of PCs you intend to calculate")
	n_pcs = adata.var.shape[0] - 1
	L.info("Setting n PCS to %i" % int(n_pcs))

There is no way to change the default n-1 in the yaml.

[wlason]

The workaround is to specify the number of PCs in the preprocessing yaml. Maybe it can be added to the documentation.

panpipes/panpipes/panpipes/pipeline_preprocess/pipeline.yml

Lines 172 to 173 in 0bc49a4

	pca: False
	n_pcs: 50