make target orgnamism modifiable

theiagen · Dec 5, 2024 · d342282 · d342282
1 parent 65e7ea8
commit d342282
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/workflows/theiacov/updates/wf_ncbi_scrub_pe.wdl b/workflows/theiacov/updates/wf_ncbi_scrub_pe.wdl
@@ -9,6 +9,7 @@ workflow dehost_pe {
     String samplename
     File read1
     File read2
+    String target_organism = "Severe acute respiratory syndrome coronavirus 2"
   }
   call ncbi_scrub.ncbi_scrub_pe {
     input:
@@ -21,7 +22,7 @@ workflow dehost_pe {
       samplename = samplename,
       read1 = ncbi_scrub_pe.read1_dehosted,
       read2 = ncbi_scrub_pe.read2_dehosted,
-      target_organism = "Severe acute respiratory syndrome coronavirus 2"
+      target_organism = target_organism
   }
   call versioning.version_capture {
     input:

diff --git a/workflows/theiacov/updates/wf_ncbi_scrub_se.wdl b/workflows/theiacov/updates/wf_ncbi_scrub_se.wdl
@@ -8,6 +8,7 @@ workflow dehost_se {
   input {
     String samplename
     File read1
+    String target_organism = "Severe acute respiratory syndrome coronavirus 2"
   }
   call ncbi_scrub.ncbi_scrub_se {
     input:
@@ -18,7 +19,7 @@ workflow dehost_se {
     input:
       samplename = samplename,
       read1 = ncbi_scrub_se.read1_dehosted,
-      target_organism = "Severe acute respiratory syndrome coronavirus 2"
+      target_organism = target_organism
   }
   call versioning.version_capture {
     input: