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main.smk: no exception when empty DGE, just warning
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danilexn committed Apr 17, 2024
1 parent 847c49e commit bf082f0
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6 changes: 0 additions & 6 deletions spacemake/snakemake/main.smk
Original file line number Diff line number Diff line change
Expand Up @@ -503,12 +503,6 @@ rule create_h5ad_dge:
)
)

if adata.X.sum() == 0:
raise SpacemakeError(f"""The h5ad file for {wildcards} is empty (adata.X.sum() == 0).
This will not be further processed.
To avoid this error from further processing other samples,
run spacemake with --keep-going""")
# add 'cell_bc' name to index for same format as individual pucks
# this also ensures compatibility with qc_sequencing_create_sheet.Rmd
adata.write(output[0])
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