Update task_nullarbor.wdl

theiagen · Dec 30, 2022 · b8098d0 · b8098d0
1 parent 685eae0
commit b8098d0
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/tasks/task_nullarbor.wdl b/tasks/task_nullarbor.wdl
@@ -59,15 +59,15 @@ task nullarbor_tsv {
       exit 1
     fi
 
-  # create file of filenames for kSNP3 input
-  touch nullarbor_input.tsv
+    # create file of filenames for nullarbor input
+    touch nullarbor_input.tsv
     for index in ${!read1_array[@]}; do
-    read1=${read1_array[$index]}
-    read2=${read2_array[$index]}
-    samplename=${samplename_array[$index]}
+      read1=${read1_array[$index]}
+      read2=${read2_array[$index]}
+      samplename=${samplename_array[$index]}
 
-    echo -e "${samplename}\t${read1}\t${read2}" >> nullarbor_input.tsv
-  done
+      echo -e "${samplename}\t${read1}\t${read2}" >> nullarbor_input.tsv
+    done
     # Run Nullarbor on the input assembly with the --all flag
     nullarbor.pl \
         --name ~{run_name} \
@@ -101,4 +101,4 @@ task nullarbor_tsv {
       disks: "local-disk 500 SSD"
       preemptible: 0
   }
-}
+}