From 4d7dd151060c7e084fc184fd42f62f6256b93f02 Mon Sep 17 00:00:00 2001
From: Wojciech Lason <40389067+wlason@users.noreply.github.com>
Date: Wed, 6 Nov 2024 17:20:08 +0000
Subject: [PATCH 1/2] Update run_scanpyQC_rna.py

Update calc_proportions default
---
 panpipes/python_scripts/run_scanpyQC_rna.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/panpipes/python_scripts/run_scanpyQC_rna.py b/panpipes/python_scripts/run_scanpyQC_rna.py
index 04e8fe5b..6befc91b 100644
--- a/panpipes/python_scripts/run_scanpyQC_rna.py
+++ b/panpipes/python_scripts/run_scanpyQC_rna.py
@@ -54,7 +54,7 @@
                     default=None,
                     help="path to file containing list of genes to quantify")
 parser.add_argument("--calc_proportions",
-                    default="mitochondrial,ribosomal",
+                    default=None,
                     help="which list of genes to use to calc proportion of mapped reads over total,per cell?")
 parser.add_argument("--score_genes",
                     default=None,
@@ -125,11 +125,12 @@
         L.error("You have not provided a list of custom genes to use for QC purposes")
         sys.exit("You have not provided a list of custom genes to use for QC purposes")
 
-for kk in calc_proportions:
-    xname= kk
-    gene_list = cat_dic[kk]
-    rna.var[xname] = [x in gene_list for x in rna.var_names] # annotate the group of hb genes as 'hb'
-    qc_vars.append(xname)
+if args.calc_proportions is not None and args.calc_proportions != 'None':
+    for kk in calc_proportions:
+        xname = kk
+        gene_list = cat_dic[kk]
+        rna.var[xname] = [x in gene_list for x in rna.var_names] # annotate the group of hb genes as 'hb'
+        qc_vars.append(xname)
 
 qc_info = ""
 if qc_vars != []:
@@ -173,4 +174,3 @@
 mdata.write(args.outfile)
 
 L.info("Done")
-

From a8fadc3cc67245466b7f8086ba890f80e9a707b8 Mon Sep 17 00:00:00 2001
From: Wojciech Lason <40389067+wlason@users.noreply.github.com>
Date: Wed, 6 Nov 2024 17:21:17 +0000
Subject: [PATCH 2/2] Update ingest pipeline.yml QC defaults

---
 panpipes/panpipes/pipeline_ingest/pipeline.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/panpipes/panpipes/pipeline_ingest/pipeline.yml b/panpipes/panpipes/pipeline_ingest/pipeline.yml
index c5ee70b5..0bf550f7 100644
--- a/panpipes/panpipes/pipeline_ingest/pipeline.yml
+++ b/panpipes/panpipes/pipeline_ingest/pipeline.yml
@@ -86,7 +86,7 @@ custom_genes_file: resources/qc_genelist_1.0.csv
 
 # (for pipeline_ingest.py)
 calc_proportions: hb,mt,rp
-score_genes: 
+score_genes: MarkersNeutro
 
 # cell cycle action
 ccgenes: default