fixed example sample map and removed docker urls from config

ETH-NEXUS · Aug 13, 2024 · b5b7329 · b5b7329
1 parent d7e9414
commit b5b7329
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/config/config.yaml b/config/config.yaml
@@ -125,13 +125,12 @@ tools:
 
   metacells:
     seacells:
-      container: "docker://mlienhard/seacells"
       # number of metacells etc need to be set here
       # increased number of metacells to 200 (default:90) since sctransform wants to calculate 100 dim pca
       params: "--n_cells=200" 
     metacells2:
-      container:  "docker://mlienhard/metacells2"
-
+      params: "" # no additional parameters to be set
+      
   remove_atypical_cells:
     # threshold type, either "number_cells" or "percentage_cells"
     threshold_type: "percentage_cells"

diff --git a/config/sample_map.tsv b/config/sample_map.tsv
@@ -1,2 +1,2 @@
-sample_name	file_stem
+sample	file_stem
 SAMPLE-1_scR	technical_long_sample.name.vXX_without_restrictions