remove uploading sorted dirs to s3

chanzuckerberg · Feb 8, 2024 · 46feed9 · 46feed9
1 parent 616494d
commit 46feed9
Showing 1 changed file with 7 additions and 8 deletions.
diff --git a/workflows/index-generation/index-generation.wdl b/workflows/index-generation/index-generation.wdl
@@ -175,10 +175,10 @@ workflow index_generation {
         File? nr_contained_in_chunk = CompressNR.contained_in_chunk
         File? nt_contained_in_tree = CompressNT.contained_in_tree
         File? nt_contained_in_chunk = CompressNT.contained_in_chunk
-        Directory? nt_split_apart_taxid_dir = CompressNT.split_apart_taxid_dir
-        Directory? nt_sorted_taxid_dir = CompressNT.sorted_taxid_dir
-        Directory? nr_split_apart_taxid_dir = CompressNR.split_apart_taxid_dir
-        Directory? nr_sorted_taxid_dir = CompressNR.sorted_taxid_dir
+    #     Directory? nt_split_apart_taxid_dir = CompressNT.split_apart_taxid_dir
+    #     Directory? nt_sorted_taxid_dir = CompressNT.sorted_taxid_dir
+    #     Directory? nr_split_apart_taxid_dir = CompressNR.split_apart_taxid_dir
+    #     Directory? nr_sorted_taxid_dir = CompressNR.sorted_taxid_dir
     }
 }
 
@@ -466,16 +466,15 @@ task CompressDatabase {
             --output-fasta ~{database_type}_compressed_shuffled.fa
 
         # Remove to save space, intermediate files are not cleaned up within a run
-        # rm -rf $READS_BY_TAXID_PATH
-        # rm -rf $SPLIT_APART_TAXID_DIR_NAME
+        rm -rf $READS_BY_TAXID_PATH
+        rm -rf $SPLIT_APART_TAXID_DIR_NAME
     >>>
 
     output {
         File compressed = "~{database_type}_compressed_shuffled.fa"
         File? contained_in_tree = "~{database_type}_contained_in_tree.tsv"
         File? contained_in_chunk = "~{database_type}_contained_in_chunk.tsv"
-        Directory split_apart_taxid_dir = "split_apart_taxid_~{database_type}"
-        Directory sorted_taxid_dir = "sorted_taxid_~{database_type}"
+        # Directory sorted_taxid_dir = "sorted_taxid_~{database_type}"
     }
 
     runtime {