just run krona merge at the end of the krakenuniq task, also specify --sample_name

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")
   }
 

pipes/WDL/workflows/classify_krakenuniq.wdl

@@ -4,12 +4,6 @@ import "../tasks/tasks_reports.wdl" as reports
 workflow classify_krakenuniq {
     call metagenomics.krakenuniq
 
-    call metagenomics.krona_merge {
-        input:
-            krona_reports = krakenuniq.krona_report_html,
-            out_basename  = "krakenuniq.krona.combined"
-    }
-
     call reports.aggregate_metagenomics_reports as metag_summary_report {
         input:
             kraken_summary_reports = krakenuniq.krakenuniq_summary_reports

pipes/WDL/workflows/demux_metag.wdl

@@ -38,11 +38,6 @@ workflow demux_metag {
       input:
         reads_unmapped_bam = illumina_demux.raw_reads_unaligned_bams
   }
-  call metagenomics.krona_merge {
-      input:
-          krona_reports = kraken.krona_report_html,
-          out_basename  = "krakenuniq.krona.combined"
-  }
   call reports.aggregate_metagenomics_reports as metag_summary_report {
       input:
           kraken_summary_reports = kraken.krakenuniq_summary_reports

pipes/WDL/workflows/demux_plus.wdl

@@ -51,12 +51,6 @@ workflow demux_plus {
             reads_unmapped_bam = illumina_demux.raw_reads_unaligned_bams
     }
 
-    call metagenomics.krona_merge {
-        input:
-            krona_reports = krakenuniq.krona_report_html,
-            out_basename  = "krakenuniq.krona.combined"
-    }
-
     call reports.spikein_summary as spike_summary {
         input:
             spikein_count_txt = spikein.report

requirements-modules.txt

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