diff --git a/workflows/theiacov/updates/wf_ncbi_scrub_pe.wdl b/workflows/theiacov/updates/wf_ncbi_scrub_pe.wdl index 7b8007351..6d4acd8ca 100644 --- 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 index 6250f65b0..23a8d707d 100644 --- 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: