Fix bug: TNseqoold.wdl

inputs

@@ -6,6 +6,8 @@
   "{{ project_name }}.normal_bam": "{{ normal_bam }}",
   "{{ project_name }}.normal_bai": "{{ normal_bai }}",
   "{{ project_name }}.normal_table": "{{ normal_table }}",
+  "{{ project_name }}.corealigner_bam": "{{ corealigner_bam }}",
+  "{{ project_name }}.corealigner_bai": "{{ corealigner_bai }}",
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.ref_dir": "{{ ref_dir }}",
   "{{ project_name }}.dbsnp": "{{ dbsnp }}",

tasks/TNseqold.wdl

@@ -3,12 +3,8 @@ task TNseqold {
   String sample
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
-  File tumor_recaled_bam
-  File tumor_recaled_bam_index
-  File tumor_recal_table
-  File normal_recaled_bam
-  File normal_recaled_bam_index
-  File normal_recal_table
+  File? corealigner_bam
+  File? corealigner_bai
   String tumor_name
   String normal_name
 
@@ -45,8 +41,7 @@ task TNseqold {
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
     $INTERVAL -r ${ref_dir}/${fasta} \
-    -i ${tumor_recaled_bam} -q ${tumor_recal_table} \
-    -i ${normal_recaled_bam} -q ${normal_recal_table} \
+    -i ${corealigner_bam} \
     --algo TNhaplotyper \
     --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
     --dbsnp ${dbsnp_dir}/${dbsnp} $PON \

workflow.wdl

@@ -6,12 +6,15 @@ import "./tasks/annovar.wdl" as annovar
 workflow {{ project_name }} {
   
   String sample_id
-  File tumor_bam
-  File tumor_bai
-  File tumor_table
-  File normal_bam
-  File normal_bai
-  File normal_table
+  File? tumor_bam
+  File? tumor_bai
+  File? tumor_table
+  File? normal_bam
+  File? normal_bai
+  File? normal_table
+
+  File? corealigner_bam
+  File? corealigner_bai
 
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
@@ -53,12 +56,8 @@ workflow {{ project_name }} {
       SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
       SENTIEON_LICENSE=SENTIEON_LICENSE,
       sample=sample_id,
-      normal_recaled_bam=normal_bam,
-      normal_recaled_bam_index=normal_bai,
-      normal_recal_table=normal_table,
-      tumor_recaled_bam=tumor_bam,
-      tumor_recaled_bam_index=tumor_bai,
-      tumor_recal_table=tumor_table,
+      corealigner_bam=corealigner_bam,
+      corealigner_bai=corealigner_bai,
       normal_name=sample_id + "_normal",
       tumor_name=sample_id + "_tumor",
       fasta=fasta,