Add krona task to TheiaMeta_Illumina_PE (#213)

* create krona task; add krona to raw and clean keaken reports in theiameta_illumina_pe * fix bug --------- Co-authored-by: Sage Wright <[email protected]>
theiagen · Nov 27, 2023 · 203ec3b · 203ec3b
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diff --git a/tasks/taxon_id/task_krona.wdl b/tasks/taxon_id/task_krona.wdl
@@ -0,0 +1,33 @@
+version 1.0
+
+task krona {
+  input {
+    File kraken2_report
+    String samplename
+    String docker = "us-docker.pkg.dev/general-theiagen/biocontainers/krona:2.7.1--pl526_5"
+    Int memory = 8
+    Int cpu = 4
+  }
+  command <<<
+    # Get VERSION
+    ktImportTaxonomy 2>&1 | sed -n '/KronaTools /p' | sed 's/^.*KronaTools //; s/ - ktImportTaxonomy.*//' | tee VERSION
+
+    # Get taxonomy file 
+    ktUpdateTaxonomy.sh taxonomy
+
+    # Run krona with taxonomy on krakren report
+    ktImportTaxonomy -o ~{samplename}_krona.html ~{kraken2_report} -tax taxonomy
+  >>>
+  output {
+    String krona_version = read_string("VERSION")
+    String krona_docker = docker
+    File krona_html = "~{samplename}_krona.html"
+  }
+  runtime {
+      docker: "~{docker}"
+      memory: "~{memory} GB"
+      cpu: cpu
+      disks: "local-disk 100 SSD"
+      preemptible: 0
+  }
+}
diff --git a/workflows/metagenomics/wf_theiameta_illumina_pe.wdl b/workflows/metagenomics/wf_theiameta_illumina_pe.wdl
@@ -3,6 +3,7 @@ version 1.0
 import "../utilities/wf_read_QC_trim_pe.wdl" as read_qc_wf
 import "../utilities/wf_metaspades_assembly.wdl" as metaspades_assembly_wf
 import "../../tasks/taxon_id/task_kraken2.wdl" as kraken_task
+import "../../tasks/taxon_id/task_krona.wdl" as krona_task
 import "../../tasks/alignment/task_minimap2.wdl" as minimap2_task
 import "../../tasks/utilities/task_parse_mapping.wdl" as parse_mapping_task
 import "../../tasks/quality_control/task_quast.wdl" as quast_task
@@ -30,6 +31,11 @@ workflow theiameta_illumina_pe {
       classified_out = "classified#.fastq",
       unclassified_out = "unclassified#.fastq"
   }
+  call krona_task.krona as krona_raw {
+    input:
+      kraken2_report = kraken2_raw.kraken2_report,
+      samplename = samplename
+  }
   call read_qc_wf.read_QC_trim_pe as read_QC_trim {
       input:
         samplename = samplename,
@@ -47,6 +53,11 @@ workflow theiameta_illumina_pe {
       classified_out = "classified#.fastq",
       unclassified_out = "unclassified#.fastq"
   }
+  call krona_task.krona as krona_clean {
+    input:
+      kraken2_report = kraken2_clean.kraken2_report,
+      samplename = samplename
+  }
   call metaspades_assembly_wf.metaspades_assembly_pe as metaspades {
     input:
       read1 = read_QC_trim.read1_clean,
@@ -134,6 +145,11 @@ workflow theiameta_illumina_pe {
     Float kraken2_percent_human_raw = kraken2_raw.kraken2_percent_human
     File kraken2_report_clean = kraken2_clean.kraken2_report
     Float kraken2_percent_human_clean = kraken2_clean.kraken2_percent_human
+    # Krona outputs
+    String krona_version = krona_raw.krona_version
+    String krona_docker = krona_raw.krona_docker
+    File krona_html_raw = krona_raw.krona_html
+    File krona_html_clean = krona_clean.krona_html
     # Read QC - dehosting outputs
     File? read1_dehosted = read_QC_trim.read1_dehosted
     File? read2_dehosted = read_QC_trim.read2_dehosted