add sort and formatting to compress_and_index_tsv

uclahs-cds · Oct 18, 2024 · 6c4f2fb · 6c4f2fb
1 parent e600366
commit 6c4f2fb
Showing 1 changed file with 4 additions and 3 deletions.
diff --git a/module/utils.nf b/module/utils.nf
@@ -49,13 +49,14 @@ process compress_and_index_tsv {
 
     script:
     """
-    bgzip ${input_tsv} --output output.tsv.gz
-    tabix -s 1 -b 2 -e 2 output.tsv.gz
+    sort ${input_tsv} > sorted_input.tsv
+    bgzip sorted_input.tsv --output output.tsv.gz
+    tabix --sequence 1 --begin 2 --end 2 output.tsv.gz
     """
 
     stub:
     """
     touch output.tsv.gz
     touch output.tsv.gz.tbi
     """
-}
+}