Update: inputs

tasks/BQSR.wdl

@@ -17,7 +17,6 @@ task BQSR {
   String cluster_config
   String disk_size
 
-  
   command <<<
     set -o pipefail
     set -e
@@ -34,7 +33,6 @@ task BQSR {
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --algo QualCal --plot --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_data.csv
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon plot bqsr -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
-
   >>>
 
   runtime {

workflow.wdl

@@ -46,13 +46,13 @@ workflow {{ project_name }} {
 
   String disk_size
   String cluster_config
-  
+
   Boolean haplotyper
   Boolean tnseq
   Boolean tnscope
   Boolean varscan
 
-  if ( tumor_fastq_1 != "" ) {
+  if (tumor_fastq_1!= "") {
     call mapping.mapping as tumor_mapping {
       input: 
       group=sample_id + '_tumor',
@@ -144,13 +144,13 @@ workflow {{ project_name }} {
       disk_size=disk_size,
       cluster_config=cluster_config
     }
-  }
+  }å
 
   call mapping.mapping as normal_mapping {
     input: 
     group=sample_id + '_normal',
     sample=sample_id + '_normal',
-    fastq_1=normal_fastq_1,
+    fastq_1=normal_fastq_1,å
     fastq_2=normal_fastq_2,
     SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
     SENTIEON_LICENSE=SENTIEON_LICENSE,