diff --git a/modules/local/templates/mtx_to_h5ad_alevin.py b/modules/local/templates/mtx_to_h5ad_alevin.py index 50107e0c..db295f1b 100755 --- a/modules/local/templates/mtx_to_h5ad_alevin.py +++ b/modules/local/templates/mtx_to_h5ad_alevin.py @@ -76,11 +76,6 @@ def input_to_adata( adata.write_h5ad(f"{output}", compression="gzip") print(f"Wrote h5ad file to {output}") - # dump versions - dump_versions() - - return adata - # # Run main script # @@ -89,8 +84,11 @@ def input_to_adata( os.makedirs("${meta.id}", exist_ok=True) # input_type comes from NF module -adata = input_to_adata( +input_to_adata( input_data="${meta.id}_alevin_results/af_quant/alevin/", output="${meta.id}/${meta.id}_${meta.input_type}_matrix.h5ad", sample="${meta.id}" ) + +# dump versions +dump_versions()