Merge pull request #40 from broadinstitute/dp-krona

add a krona_merge task

Author: dpark01

pipes/WDL/tasks/tasks_metagenomics.wdl

@@ -40,7 +40,7 @@ task krakenuniq {
     OUT_BASENAME=basenames_reports.txt
     for bam in ${sep=' ' reads_unmapped_bam}; do
       echo "$(basename $bam .bam).krakenuniq-reads.txt.gz" >> $OUT_READS
-      echo "$(basename $bam .bam).krakenuniq" >> $OUT_BASENAME
+      echo "$(basename $bam .bam)" >> $OUT_BASENAME
       echo "$(basename $bam .bam).krakenuniq-summary_report.txt" >> $OUT_REPORTS
     done
 
@@ -62,18 +62,23 @@ task krakenuniq {
     # run single-threaded krona on up to nproc samples at once
     parallel -I ,, \
       "metagenomics.py krona \
-        ,,-summary_report.txt \
+        ,,.krakenuniq-summary_report.txt \
         $DB_DIR/krona \
-        ,,-krona.html \
+        ,,.krakenuniq-krona.html \
+        --sample_name ,, \
         --noRank --noHits --inputType krakenuniq \
         --loglevel=DEBUG" \
       ::: `cat $OUT_BASENAME`
+
+    # merge all krona reports
+    ktImportKrona -o krakenuniq.krona.combined.html *.krakenuniq-krona.html
   }
 
   output {
     Array[File] krakenuniq_classified_reads   = glob("*.krakenuniq-reads.txt.gz")
     Array[File] krakenuniq_summary_reports    = glob("*.krakenuniq-summary_report.txt")
     Array[File] krona_report_html             = glob("*.krakenuniq-krona.html")
+    File        krona_report_merged_html      = "krakenuniq.krona.combined.html"
     String      viralngs_version              = read_string("VERSION")
   }
 
@@ -302,10 +307,6 @@ task krona {
 
   String  input_basename = basename(classified_reads_txt_gz, ".txt.gz")
 
-#  parameter_meta {
-#    krona_taxonomy_db_tgz : "stream"
-#  }
-
   command {
     set -ex -o pipefail
     DB_DIR=$(mktemp -d --suffix _db)
@@ -338,9 +339,35 @@ task krona {
 
   runtime {
     docker: "${docker}"
-    memory: "4 GB"
+    memory: "3 GB"
+    cpu: 1
+    disks: "local-disk 50 HDD"
+    dx_instance_type: "mem1_ssd2_v2_x2"
+  }
+}
+
+task krona_merge {
+  Array[File]  krona_reports
+  String       out_basename
+
+  String?      docker="biocontainers/krona:v2.7.1_cv1"
+
+  command {
+    set -ex -o pipefail
+    ktImportKrona | head -2 | tail -1 | cut -f 2-3 -d ' ' | tee VERSION
+    ktImportKrona -o "${out_basename}.html" ${sep=' ' krona_reports}
+  }
+
+  output {
+    File    krona_report_html = "${out_basename}.html"
+    String  krona_version     = read_string("VERSION")
+  }
+
+  runtime {
+    docker: "${docker}"
+    memory: "3 GB"
     cpu: 1
-    disks: "local-disk 50 SSD"
+    disks: "local-disk 50 HDD"
     dx_instance_type: "mem1_ssd2_v2_x2"
   }
 }

pipes/WDL/workflows/classify_kraken.wdl

@@ -1,4 +1,4 @@
 broadinstitute/viral-core=v2.0.20.1
 broadinstitute/viral-assemble=v2.0.17.0
-broadinstitute/viral-classify=v2.0.16.0
+broadinstitute/viral-classify=v2.0.20.2
 broadinstitute/viral-phylo=v2.0.16.0