diff --git a/benj/aggregate.py b/benj/aggregate.py index d0c15c7..31fddc6 100644 --- a/benj/aggregate.py +++ b/benj/aggregate.py @@ -165,11 +165,15 @@ def aggregate_concat(metadata=None, directory:Union[_PathLike, List[_PathLike]]= for sample in tqdm(metadata.index.values): ### TODO sample may be aggr not actual sample ### find sample checks 1: h5ad 2: directory+metadata, 3: sample.h5ad - adata, fname = find_sample(directory=directory, h5ad=h5ad.get(sample), - sample=sample, metadata=metadata, qc=calc_qc, - min_cells_per_sample=min_cells_per_sample, - verbose=verbose, - **kwargs) + try: + adata, fname = find_sample(directory=directory, h5ad=h5ad.get(sample), + sample=sample, metadata=metadata, qc=calc_qc, + min_cells_per_sample=min_cells_per_sample, + verbose=verbose, + **kwargs) + except: + adata = None + pass if adata is None: bad.append(sample) else: