squidpy fix nfs error

goeckslab · Jun 24, 2024 · 1125674 · 1125674
1 parent 9fb5578
commit 1125674
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/tools/squidpy/squidpy_spatial.xml b/tools/squidpy/squidpy_spatial.xml
@@ -19,7 +19,9 @@
             #if $analyses.selected_tool in ['nhood_enrichment', 'centrality_scores', 'interaction_matrix', 'ligrec', 'ripley', 'co_occurrence']:
             --output_plot "`pwd`/image.png"
             #end if
-
+        #if $analyses.selected_tool in ['nhood_enrichment', 'centrality_scores', 'interaction_matrix', 'ligrec', 'ripley', 'co_occurrence']:
+            && mv "`pwd`/image.png" "final_image.png"
+        #end if
         ]]>
     </command>
     <configfiles>
@@ -246,7 +248,7 @@
     </inputs>
     <outputs>
         <data format="h5ad" name="output" label="Squidpy.gr.${analyses.selected_tool} on ${on_string}" />
-        <data from_work_dir="image.png" format="png" name="output_plot" label="Squidpy.pl.${analyses.selected_tool} on ${on_string}" >
+        <data from_work_dir="final_image.png" format="png" name="output_plot" label="Squidpy.pl.${analyses.selected_tool} on ${on_string}" >
             <filter>analyses['selected_tool'] in ['nhood_enrichment', 'centrality_scores', 'interaction_matrix', 'ligrec', 'ripley', 'co_occurrence']</filter>
         </data>
     </outputs>