From 54fa0fe603641ca7476b00e7395f1904eb3e62ef Mon Sep 17 00:00:00 2001 From: SarahOuologuem Date: Wed, 29 Nov 2023 10:48:36 +0100 Subject: [PATCH 1/2] Update mdata --- panpipes/python_scripts/run_scanpyQC_rna.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/panpipes/python_scripts/run_scanpyQC_rna.py b/panpipes/python_scripts/run_scanpyQC_rna.py index be49aaf0..bc66c419 100644 --- a/panpipes/python_scripts/run_scanpyQC_rna.py +++ b/panpipes/python_scripts/run_scanpyQC_rna.py @@ -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") From 80b6da46cc92f5ad10ce69525d24545bcb64ed5b Mon Sep 17 00:00:00 2001 From: SarahOuologuem Date: Wed, 29 Nov 2023 10:49:11 +0100 Subject: [PATCH 2/2] Add scr_run --- panpipes/panpipes/pipeline_ingest.py | 1 + 1 file changed, 1 insertion(+) diff --git a/panpipes/panpipes/pipeline_ingest.py b/panpipes/panpipes/pipeline_ingest.py index 5bee1e69..3ea6f3aa 100644 --- a/panpipes/panpipes/pipeline_ingest.py +++ b/panpipes/panpipes/pipeline_ingest.py @@ -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"))