forgot about the ncbi_scrub standalone wfs again

theiagen · Oct 25, 2024 · 6e7e0ef · 6e7e0ef
1 parent 283d7e1
commit 6e7e0ef
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Showing 2 changed files with 18 additions and 10 deletions.
diff --git a/workflows/theiacov/updates/wf_ncbi_scrub_pe.wdl b/workflows/theiacov/updates/wf_ncbi_scrub_pe.wdl
@@ -9,18 +9,22 @@ workflow dehost_pe {
     String samplename
     File read1
     File read2
+    File kraken2_db = "gs://theiagen-large-public-files-rp/terra/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz"
+
   }
   call ncbi_scrub.ncbi_scrub_pe {
     input:
       samplename = samplename,
       read1 = read1,
       read2 = read2
   }
-  call kraken.kraken2_theiacov as kraken2 {
+  call kraken.kraken2_standalone as kraken2 {
     input:
       samplename = samplename,
       read1 = ncbi_scrub_pe.read1_dehosted,
-      read2 = ncbi_scrub_pe.read2_dehosted
+      read2 = ncbi_scrub_pe.read2_dehosted,
+      kraken2_db = kraken2_db,
+      target_organism = "Severe acute respiratory syndrome coronavirus 2"
   }
   call versioning.version_capture {
     input:
@@ -32,9 +36,9 @@ workflow dehost_pe {
     File read2_dehosted = ncbi_scrub_pe.read2_dehosted
     Int ncbi_scrub_human_spots_removed = ncbi_scrub_pe.human_spots_removed
     String ncbi_scrub_docker = ncbi_scrub_pe.ncbi_scrub_docker
-    Float kraken2_human_dehosted = kraken2.percent_human
-    Float kraken2_sc2_dehosted = kraken2.percent_sc2
+    Float kraken2_human_dehosted = kraken2.kraken2_percent_human
+    Float kraken2_sc2_dehosted = kraken2.kraken2_percent_sc2
     File kraken2_report_dehosted = kraken2.kraken2_report
-    String kraken2_version_dehosted = kraken2.version
+    String kraken2_version_dehosted = kraken2.kraken2_version
   }
 }
diff --git a/workflows/theiacov/updates/wf_ncbi_scrub_se.wdl b/workflows/theiacov/updates/wf_ncbi_scrub_se.wdl
@@ -8,16 +8,20 @@ workflow dehost_se {
   input {
     String samplename
     File read1
+    File kraken2_db = "gs://theiagen-large-public-files-rp/terra/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz"
+
   }
   call ncbi_scrub.ncbi_scrub_se {
     input:
       samplename = samplename,
       read1 = read1
   }
-  call kraken.kraken2_theiacov as kraken2 {
+  call kraken.kraken2_standalone as kraken2 {
     input:
       samplename = samplename,
-      read1 = ncbi_scrub_se.read1_dehosted
+      read1 = ncbi_scrub_se.read1_dehosted,
+      kraken2_db = kraken2_db,
+      target_organism = "Severe acute respiratory syndrome coronavirus 2"
   }
   call versioning.version_capture {
     input:
@@ -28,9 +32,9 @@ workflow dehost_se {
     File read1_dehosted = ncbi_scrub_se.read1_dehosted
     String ncbi_scrub_docker = ncbi_scrub_se.ncbi_scrub_docker
     Int ncbi_scrub_human_spots_removed = ncbi_scrub_se.human_spots_removed
-    Float kraken2_human_dehosted = kraken2.percent_human
-    Float kraken2_sc2_dehosted = kraken2.percent_sc2
-    String kraken2_version_dehosted = kraken2.version
+    Float kraken2_human_dehosted = kraken2.kraken2_percent_human
+    Float kraken2_sc2_dehosted = kraken2.kraken2_percent_sc2
+    String kraken2_version_dehosted = kraken2.kraken2_version
     File kraken2_report_dehosted = kraken2.kraken2_report
   }
 }