fix formatting

theiagen · Apr 20, 2021 · dd967de · dd967de
1 parent b350e1d
commit dd967de
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Showing 2 changed files with 8 additions and 6 deletions.
diff --git a/workflows/wf_ncbi_scrub_pe.wdl b/workflows/wf_ncbi_scrub_pe.wdl
@@ -1,6 +1,7 @@
 version 1.0
 
 import "../tasks/task_read_clean.wdl" as read_clean
+import "../tasks/task_taxonID.wdl" as taxonID
 
 workflow dehost_pe {
 	input {
@@ -18,18 +19,18 @@ workflow dehost_pe {
 	  call taxonID.kraken2 {
 	    input:
 	      samplename = samplename,
-	      read1 = ncbi_scrub_pe.read1_dehosted
+	      read1 = ncbi_scrub_pe.read1_dehosted,
 				read2 = ncbi_scrub_pe.read2_dehosted
 	  }
 
 	output {
 			File	read1_dehosted	=	ncbi_scrub_pe.read1_dehosted
 			File 	read2_dehosted	=	ncbi_scrub_pe.read2_dehosted
 			String	ncbi_scrub_docker	=	ncbi_scrub_pe.ncbi_scrub_docker
+
 			Float	kraken_human_dehosted	=	kraken2.percent_human
 			Float	kraken_sc2_dehosted	=	kraken2.percent_sc2
 			String	kraken_report_dehosted	=	kraken2.kraken_report
 			String	kraken_version_dehosted	=	kraken2.version
-			String	kraken_report_dehosted	=	kraken2.kraken_report
 	}
 }
diff --git a/workflows/wf_ncbi_scrub_se.wdl b/workflows/wf_ncbi_scrub_se.wdl
@@ -1,6 +1,7 @@
 version 1.0
 
 import "../tasks/task_read_clean.wdl" as read_clean
+import "../tasks/task_taxonID.wdl" as taxonID
 
 workflow dehost_se {
 	input {
@@ -16,14 +17,14 @@ workflow dehost_se {
 	call taxonID.kraken2 {
 		input:
 			samplename = samplename,
-			read1 = ncbi_scrub_pe.read1_dehosted
+			read1 = ncbi_scrub_se.read1_dehosted
 	}
 	output {
-			File	reads_dehosted	=	ncbi_scrub_pe.read1_dehosted
-			String	ncbi_scrub_docker	=	ncbi_scrub_pe.ncbi_scrub_docker
+			File	reads_dehosted	=	ncbi_scrub_se.read1_dehosted
+			String	ncbi_scrub_docker	=	ncbi_scrub_se.ncbi_scrub_docker
+
 			Float	kraken_human_dehosted	=	kraken2.percent_human
 			Float	kraken_sc2_dehosted	=	kraken2.percent_sc2
-			String	kraken_report_dehosted	=	kraken2.kraken_report
 			String	kraken_version_dehosted	=	kraken2.version
 			String	kraken_report_dehosted	=	kraken2.kraken_report
 	}