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Small code fixes in panpipes_ingest #144

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merged 2 commits into from
Nov 29, 2023
Merged

Small code fixes in panpipes_ingest #144

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54fa0fe
Update mdata
SarahOuologuem Nov 29, 2023
80b6da4
Add scr_run
SarahOuologuem Nov 29, 2023
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1 change: 1 addition & 0 deletions panpipes/panpipes/pipeline_ingest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -313,6 +313,7 @@ def concat_bg_mudatas(infiles, outfile):

def orfile():
return PARAMS['sample_prefix'] + "_cell_metadata.tsv"
@active_if(PARAMS["scr_run"])
@active_if(PARAMS['modalities_rna'])
@active_if(PARAMS["use_existing_h5mu"] is False)
@follows(mkdir("scrublet"))
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2 changes: 2 additions & 0 deletions panpipes/python_scripts/run_scanpyQC_rna.py
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Expand Up @@ -159,6 +159,8 @@

L.info("calculated scores and metrics")

mdata.update()

L.info("saving anndata and obs in a metadata tsv file")
write_obs(mdata, output_prefix=args.sampleprefix,
output_suffix="_cell_metadata.tsv")
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