diff --git a/workflows/utilities/wf_read_QC_trim_ont.wdl b/workflows/utilities/wf_read_QC_trim_ont.wdl
index 99dd0112e..34765fa9c 100644
--- a/workflows/utilities/wf_read_QC_trim_ont.wdl
+++ b/workflows/utilities/wf_read_QC_trim_ont.wdl
@@ -29,11 +29,11 @@ workflow read_QC_trim_ont {
 
     # kraken inputs
     String? target_organism
-    Boolean call_kraken = false
-    Int? kraken_disk_size
-    Int? kraken_memory
-    Int? kraken_cpu
-    File? kraken_db
+    Boolean call_kraken2 = false
+    Int? kraken2_disk_size
+    Int? kraken2_memory
+    Int? kraken2_cpu
+    File? kraken2_db
 
     # rasusa downsampling
     Float downsampling_coverage = 150
@@ -57,7 +57,7 @@ workflow read_QC_trim_ont {
         samplename = samplename,
         read1 = read1,
         target_organism = target_organism,
-        kraken2_db = select_first([kraken_db])
+        kraken2_db = select_first([kraken2_db])
     }
     call kraken2.kraken2_parse_classified as kraken2_recalculate_abundances_raw {
       input:
@@ -71,7 +71,7 @@ workflow read_QC_trim_ont {
         samplename = samplename,
         read1 = ncbi_scrub_se.read1_dehosted,
         target_organism = target_organism,
-        kraken2_db = select_first([kraken_db])
+        kraken2_db = select_first([kraken2_db])
     }
     call kraken2.kraken2_parse_classified as kraken2_recalculate_abundances_dehosted {
       input:
@@ -82,15 +82,15 @@ workflow read_QC_trim_ont {
     } 
   }
   if ("~{workflow_series}" == "theiaprok") {
-    if ((call_kraken) && defined(kraken_db)) {
+    if ((call_kraken2) && defined(kraken2_db)) {
       call kraken2.kraken2_standalone as kraken2_theiaprok {
         input:
           samplename = samplename,
           read1 = read1,
-          kraken2_db = select_first([kraken_db]),
-          disk_size = kraken_disk_size,
-          memory = kraken_memory,
-          cpu = kraken_cpu
+          kraken2_db = select_first([kraken2_db]),
+          disk_size = kraken2_disk_size,
+          memory = kraken2_memory,
+          cpu = kraken2_cpu
       }
       call kraken2.kraken2_parse_classified as kraken2_recalculate_abundances {
         input:
@@ -98,8 +98,8 @@ workflow read_QC_trim_ont {
           kraken2_report = kraken2_theiaprok.kraken2_report,
           kraken2_classified_report = kraken2_theiaprok.kraken2_classified_report
       }
-    } if ((call_kraken) && ! defined(kraken_db)) {
-      String kraken_db_warning = "Kraken database not defined"
+    } if ((call_kraken2) && ! defined(kraken2_db)) {
+      String kraken2_db_warning = "Kraken2 database not defined"
     }
 
     # rasusa for random downsampling
@@ -140,7 +140,7 @@ workflow read_QC_trim_ont {
     String? kraken2_sc2_dehosted = kraken2_recalculate_abundances_dehosted.percent_sc2
     String? kraken2_target_organism_dehosted = kraken2_recalculate_abundances_dehosted.percent_target_organism
     File? kraken2_report_dehosted = kraken2_recalculate_abundances_dehosted.kraken_report
-    String kraken2_database = select_first([kraken2_theiacov_raw.kraken2_database, kraken2_theiaprok.kraken2_database, kraken_db_warning, ""])
+    String kraken2_database = select_first([kraken2_theiacov_raw.kraken2_database, kraken2_theiaprok.kraken2_database, kraken2_db_warning, ""])
    
     # estimated genome length -- by default for TheiaProk this is 5Mb
     Int est_genome_length = genome_length
diff --git a/workflows/utilities/wf_read_QC_trim_pe.wdl b/workflows/utilities/wf_read_QC_trim_pe.wdl
index 836dc5fea..57ea3fe36 100644
--- a/workflows/utilities/wf_read_QC_trim_pe.wdl
+++ b/workflows/utilities/wf_read_QC_trim_pe.wdl
@@ -24,11 +24,11 @@ workflow read_QC_trim_pe {
     Int bbduk_memory = 8
     Boolean call_midas = false
     File? midas_db
-    Boolean call_kraken = false
-    Int? kraken_disk_size
-    Int? kraken_memory
-    Int? kraken_cpu
-    File? kraken_db
+    Boolean call_kraken2 = false
+    Int? kraken2_disk_size
+    Int? kraken2_memory
+    Int? kraken2_cpu
+    File? kraken2_db
     String? target_organism
     File? adapters
     File? phix
@@ -53,7 +53,7 @@ workflow read_QC_trim_pe {
         read1 = read1,
         read2 = read2,
         target_organism = target_organism,
-        kraken2_db = select_first([kraken_db])
+        kraken2_db = select_first([kraken2_db])
     }
     call kraken.kraken2_standalone as kraken2_theiacov_dehosted {
       input:
@@ -61,7 +61,7 @@ workflow read_QC_trim_pe {
         read1 = select_first([ncbi_scrub_pe.read1_dehosted]),
         read2 = ncbi_scrub_pe.read2_dehosted,
         target_organism = target_organism,
-        kraken2_db = select_first([kraken_db])
+        kraken2_db = select_first([kraken2_db])
     }
   }
   if (read_processing == "trimmomatic") {
@@ -133,19 +133,19 @@ workflow read_QC_trim_pe {
     }
   }
   if ("~{workflow_series}" == "theiaprok") {
-    if ((call_kraken) && defined(kraken_db)) {
+    if ((call_kraken2) && defined(kraken2_db)) {
       call kraken.kraken2_standalone as kraken2_theiaprok {
         input:
           samplename = samplename,
           read1 = read1,
           read2 = read2,
-          kraken2_db = select_first([kraken_db]),
-          disk_size = kraken_disk_size,
-          memory = kraken_memory,
-          cpu = kraken_cpu
+          kraken2_db = select_first([kraken2_db]),
+          disk_size = kraken2_disk_size,
+          memory = kraken2_memory,
+          cpu = kraken2_cpu
       }
-    }  if ((call_kraken) && ! defined(kraken_db)) {
-      String kraken_db_warning = "Kraken database not defined"
+    }  if ((call_kraken2) && ! defined(kraken2_db)) {
+      String kraken2_db_warning = "Kraken2 database not defined"
     }
   }
   if ("~{workflow_series}" == "theiameta") {
@@ -203,7 +203,7 @@ workflow read_QC_trim_pe {
     String? kraken2_target_organism_name = target_organism
     File? kraken2_report_dehosted = kraken2_theiacov_dehosted.kraken2_report
     String kraken2_docker = select_first([kraken2_theiacov_raw.kraken2_docker, kraken2_theiaprok.kraken2_docker, ""])
-    String kraken2_database = select_first([kraken2_theiacov_raw.kraken2_database, kraken2_theiaprok.kraken2_database, kraken_db_warning, ""])
+    String kraken2_database = select_first([kraken2_theiacov_raw.kraken2_database, kraken2_theiaprok.kraken2_database, kraken2_db_warning, ""])
     
     # trimming versioning
     String? trimmomatic_version = trimmomatic_pe.version
diff --git a/workflows/utilities/wf_read_QC_trim_se.wdl b/workflows/utilities/wf_read_QC_trim_se.wdl
index 6b193d8c3..dae1f254f 100644
--- a/workflows/utilities/wf_read_QC_trim_se.wdl
+++ b/workflows/utilities/wf_read_QC_trim_se.wdl
@@ -27,11 +27,11 @@ workflow read_QC_trim_se {
     String? trimmomatic_args
     Boolean call_midas = false
     File? midas_db
-    Boolean call_kraken = false
-    File? kraken_db
-    Int? kraken_disk_size
-    Int? kraken_memory
-    Int? kraken_cpu
+    Boolean call_kraken2 = false
+    File? kraken2_db
+    Int? kraken2_disk_size
+    Int? kraken2_memory
+    Int? kraken2_cpu
     String read_processing = "trimmomatic" # options: trimmomatic, fastp
     String read_qc = "fastq_scan" # options: fastq_scan, fastqc
     String fastp_args = "-g -5 20 -3 20"
@@ -101,14 +101,14 @@ workflow read_QC_trim_se {
         samplename = samplename,
         read1 = read1,
         target_organism = target_organism,
-        kraken2_db = select_first([kraken_db])
+        kraken2_db = select_first([kraken2_db])
     }
     call kraken.kraken2_standalone as kraken2_theiacov_dehosted {
       input:
         samplename = samplename,
         read1 = select_first([ncbi_scrub_se.read1_dehosted]),
         target_organism = target_organism,
-        kraken2_db = select_first([kraken_db])
+        kraken2_db = select_first([kraken2_db])
     }
   }
   if ("~{workflow_series}" == "theiaprok") {
@@ -122,18 +122,18 @@ workflow read_QC_trim_se {
     }
   }
   if ("~{workflow_series}" == "theiaprok") {
-    if ((call_kraken) && defined(kraken_db)) {
+    if ((call_kraken2) && defined(kraken2_db)) {
       call kraken.kraken2_standalone as kraken2_theiaprok {
         input:
           samplename = samplename,
           read1 = read1,
-          kraken2_db = select_first([kraken_db]),
-          disk_size = kraken_disk_size,
-          memory = kraken_memory,
-          cpu = kraken_cpu
+          kraken2_db = select_first([kraken2_db]),
+          disk_size = kraken2_disk_size,
+          memory = kraken2_memory,
+          cpu = kraken2_cpu
       }
-    }  if ((call_kraken) && ! defined(kraken_db)) {
-      String kraken_db_warning = "Kraken database not defined"
+    }  if ((call_kraken2) && ! defined(kraken2_db)) {
+      String kraken2_db_warning = "Kraken database not defined"
     }
   }
   output {
@@ -172,7 +172,7 @@ workflow read_QC_trim_se {
     String? kraken2_target_organism_name = target_organism
     File? kraken2_report_dehosted = kraken2_theiacov_dehosted.kraken2_report
     String kraken2_docker = select_first([kraken2_theiacov_raw.kraken2_docker, kraken2_theiaprok.kraken2_docker, ""])
-    String kraken2_database = select_first([kraken2_theiacov_raw.kraken2_database, kraken2_theiaprok.kraken2_database, kraken_db_warning, ""])
+    String kraken2_database = select_first([kraken2_theiacov_raw.kraken2_database, kraken2_theiaprok.kraken2_database, kraken2_db_warning, ""])
    
     # trimming versioning
     String? trimmomatic_version = trimmomatic_se.version