trying to fix mapping report issue

BleekerLab · Sep 15, 2020 · 66fd7e4 · 66fd7e4
1 parent 9052737
commit 66fd7e4
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/Snakefile b/Snakefile
@@ -185,7 +185,7 @@ rule map_to_genome_using_STAR:
 
 rule generate_mapping_summary:
     input:
-        directory(RESULT_DIR + "star/")
+        RESULT_DIR + "star/{sample}_Log.final.out"
     output:
         RESULT_DIR + "star/mapping_summary.tsv"
     message:

diff --git a/scripts/generate_mapping_summary.py b/scripts/generate_mapping_summary.py
@@ -14,7 +14,7 @@
 # Reads each file. Add sample name in the column with values
 ############################################################
 
-list_of_logs = [f for f in os.listdir(directory_with_mapping_reports) if f.endswith("Log.final.out")]
+list_of_logs = [directory_with_mapping_reports + f for f in os.listdir(directory_with_mapping_reports) if f.endswith("Log.final.out")]
 list_of_logs.sort()