mummer_ani task: added percent_base_aligned_threshold with 70 as defa…

…ult. default ani_threshold is now 85. Also added logic to only output ani_top_species_match if both thresholds are surpassed.

tasks/quality_control/task_mummer_ani.wdl

@@ -6,7 +6,9 @@ task animummer {
     String samplename
     File? ref_genome
     Float mash_filter = 0.9
-    Float ani_threshold = 92.0
+    # these 2 thresholds were set as they are used by CDC enterics lab/PulseNet for ANI thresholds
+    Float ani_threshold = 85.0
+    Float percent_bases_aligned_threshold = 70.0
     String docker= "us-docker.pkg.dev/general-theiagen/staphb/mummer:4.0.0-rgdv2"
     Int cpus = 4
     Int memory = 8
@@ -53,6 +55,7 @@ task animummer {
       ## parse out highest percentBases aligned
       cut -f 5 ~{samplename}.ani-mummer.out.tsv | sort -nr | head -n 1 | tee ANI_HIGHEST_PERCENT_BASES_ALIGNED.txt
       echo "highest percent bases aligned is: $(cat ANI_HIGHEST_PERCENT_BASES_ALIGNED.txt)"
+      ANI_HIGHEST_PERCENT_BASES_ALIGNED=$(cat ANI_HIGHEST_PERCENT_BASES_ALIGNED.txt)
 
       ## parse out ANI value using highest percentBases aligned value
       grep "$(cat ANI_HIGHEST_PERCENT_BASES_ALIGNED.txt)" ~{samplename}.ani-mummer.out.tsv | cut -f 3 | tee ANI_HIGHEST_PERCENT.txt
@@ -72,15 +75,21 @@ task animummer {
         grep "${ANI_HIGHEST_PERCENT}" ~{samplename}.ani-mummer.out.tsv | cut -f 1,2 | sed "s|${assembly_file_basename}||g" | xargs | cut -d '.' -f 3 | tee ANI_TOP_SPECIES_MATCH.txt
         echo "ANI top species match is: $(cat ANI_TOP_SPECIES_MATCH.txt)"
 
-        # if ANI threshold is defined by user, compare to highest ANI value and only output if threshold is surpassed
-        if [[ -n "~{ani_threshold}" ]]; then
+        # if ANI threshold or percent_bases_aligned_threshold is defined by user (they both are by default), compare to highest ANI value and corresponding percent_bases_aligned value and only output ANI_top_species_match if both thresholds are surpassed
+        if [[ -n "~{ani_threshold}" || -n "~{percent_bases_aligned_threshold}" ]]; then
           echo "Comparing user-defined ANI threshold to highest ANI value..."
           # compare ANI_HIGHEST_PERCENT to ani_threshold using awk
           if ! awk "BEGIN{ exit ($ANI_HIGHEST_PERCENT < ~{ani_threshold} )}"; then
             echo "The highest ANI value $ANI_HIGHEST_PERCENT is less than the user-defined threshold of ~{ani_threshold}"
             echo "ANI top species match did not surpass the user-defined threshold of ~{ani_threshold}" > ANI_TOP_SPECIES_MATCH.txt
+          # else if: compare percent_bases_aligned_threshold to ANI_HIGHEST_PERCENT_BASES_ALIGNED using awk
+          elif ! awk "BEGIN{ exit (${ANI_HIGHEST_PERCENT_BASES_ALIGNED} < ~{percent_bases_aligned_threshold} )}"; then
+            echo "The highest ANI percent bases aligned value ${ANI_HIGHEST_PERCENT_BASES_ALIGNED} is less than the user-defined threshold of ~{percent_bases_aligned_threshold}"
+            # overwrite ANI_TOP_SPECIES_MATCH.txt when percent_bases_aligned threshold is not surpassed
+            echo "ANI percent bases aligned did not surpass the user-defined threshold of ~{percent_bases_aligned_threshold}" > ANI_TOP_SPECIES_MATCH.txt 
           else
-            echo "The highest ANI value $ANI_HIGHEST_PERCENT is greater than the user-defined threshold ~{ani_threshold}"
+            echo "The highest ANI value ${ANI_HIGHEST_PERCENT} is greater than the user-defined threshold ~{ani_threshold}"
+            echo "The highest percent bases aligned value ${ANI_HIGHEST_PERCENT_BASES_ALIGNED} is greater than the user-defined threshold ~{percent_bases_aligned_threshold}"
           fi
         fi
       else