renamed /python/run_scanpyQC_REP.py & commented out barcode_mtd args …

[deevdevil88]

made changes to deal with #2 and also made changes to panpipes_qc_mm.py for bg_concat and commented out barcode_mtd related args.

Best,
Devika

[deevdevil88]

also we updated make_adata_from_csv.py to update the prot modality to not have the hashing_ab info, so that that making adata objects doesnt error.

[deevdevil88]

While trying to change the defaults for scvi model_args for RNA in panpipes_integration.py, noticed that the pipeline.yml had the args n_latent and n_layers as they should be called based on https://docs.scvi-tools.org/en/0.20.1/api/reference/scvi.model.SCVI.html written as nlatent and nlayers. This was causing the pipeline to error, as model_args are called as is in the batch_correct_scvi.pyscript on line 142

[deevdevil88]

Added harmony sigma and harmony_pcs model_args to ruffus in pipeline_integration.py for rna and prot and atact modalities, and also changed neighbors_n_pcs to neighbors_ndims in all places for harmony to clarify between harmony pcs and neighbor dims.

[deevdevil88]

After making changes to batch_correct_harmony.py for neighbours_npcs to neighbours_ndims, had to change npcs to ndims in batch_correct_wnn.py for when using harmony neighbours for the modailities. see screenshot of error

[deevdevil88]

as neighbours_n_pcs is a PARAM for all methods, this has been reverted back to its original and only harmony_npcs has been added.

[deevdevil88]

parameterised sigma paramter for batch correction with Harmony.

[crichgriffin]

All good, I will merge with the master

[crichgriffin]

Approved