Merging with Batch Keys

[SandwichFiend]

Hello,

I'm having trouble merging samples with Batch Keys as described in the ReadMe. I'm trying to execute the following:

#Define Batch Keys
BKeys = ["sample"]

#Merge the TCR Data
!python /content/conga/scripts/merge_samples.py
--samples /content/drive/MyDrive/R_Data/Samples.txt
--output_clones_file merged_pbmc_clones.tsv
--output_gex_data merged_pbmc_gex.h5ad
--organism mouse
--batch_keys BKeys

My samples file is formatted as follows:
clones_file gex_data gex_data_type sample
/content/S1_clones.tsv /content/drive/MyDrive/R_Data/S1_mtx 10x_mtx 1
/content/S2_clones.tsv /content/drive/MyDrive/R_Data/S2_mtx 10x_mtx 2

This throws the following error:
/usr/local/lib/python3.7/dist-packages/statsmodels/tools/_testing.py:19: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
import pandas.util.testing as tm
reading: /content/drive/MyDrive/R_Data/S1_mtx of type 10x_mtx
/content/conga/conga/preprocess.py:226: DeprecationWarning: Use is_view instead of isview, isview will be removed in the future.
if adata.isview: # ran into trouble with AnnData views vs copies
Traceback (most recent call last):
File "/content/conga/scripts/merge_samples.py", line 91, in
assert k in df.columns
AssertionError

This code will complete successfully without the batch keys flag. What am I doing wrong?

Thanks!

[SandwichFiend]

Update: Made 2 changes and it worked.

1. Changed .txt file to .tsv file
2. Changed --batch_keys BKeys to --batch_keys 'sample'

I guess it didn't like one of those things.

Thanks for the cool package!