Alter: TNseq Input

tasks/Realigner.wdl

@@ -36,8 +36,8 @@ task Realigner {
   }
 
   output {
-    File realigner_bam = "${sample}.sorted.deduped.realigned.bam"
-    File realigner_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"
+    File realigned_bam = "${sample}.sorted.deduped.realigned.bam"
+    File realigned_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"
 
   }
 }

tasks/TNseq.wdl

@@ -3,11 +3,11 @@ task TNseq {
   String sample
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
-  File tumor_recaled_bam
-  File tumor_recaled_bam_index
+  File tumor_realigned_bam
+  File tumor_realigned_bam_index
   File tumor_recal_table
-  File normal_recaled_bam
-  File normal_recaled_bam_index
+  File normal_realigned_bam
+  File normal_realigned_bam_index
   File normal_recal_table
   String tumor_name
   String normal_name
@@ -45,8 +45,8 @@ task TNseq {
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
     -r ${ref_dir}/${fasta} $INTERVAL \
-    -i ${tumor_recaled_bam} -q ${tumor_recal_table} \
-    -i ${normal_recaled_bam} -q ${normal_recal_table} \
+    -i ${tumor_realigned_bam} -q ${tumor_recal_table} \
+    -i ${normal_realigned_bam} -q ${normal_recal_table} \
     --algo TNhaplotyper2 \
     --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
     --germline_vcf ${germline_resource} \

workflow.wdl

@@ -130,8 +130,8 @@ workflow {{ project_name }} {
       SENTIEON_LICENSE=SENTIEON_LICENSE,
       fasta=fasta,
       ref_dir=ref_dir,
-      realigned_bam=tumor_Realigner.realigner_bam,
-      realigned_bam_index=tumor_Realigner.realigner_bam_index,
+      realigned_bam=tumor_Realigner.realigned_bam,
+      realigned_bam_index=tumor_Realigner.realigned_bam_index,
       db_mills=db_mills,
       dbmills_dir=dbmills_dir,
       dbsnp=dbsnp,
@@ -223,8 +223,8 @@ workflow {{ project_name }} {
     SENTIEON_LICENSE=SENTIEON_LICENSE,
     fasta=fasta,
     ref_dir=ref_dir,
-    realigned_bam=normal_Realigner.realigner_bam,
-    realigned_bam_index=normal_Realigner.realigner_bam_index,
+    realigned_bam=normal_Realigner.realigned_bam,
+    realigned_bam_index=normal_Realigner.realigned_bam_index,
     db_mills=db_mills,
     dbmills_dir=dbmills_dir,
     dbsnp=dbsnp,
@@ -261,11 +261,11 @@ workflow {{ project_name }} {
       SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
       SENTIEON_LICENSE=SENTIEON_LICENSE,
       sample=sample_id,
-      normal_recaled_bam=normal_BQSR.recaled_bam,
-      normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
+      normal_realigned_bam=normal_Realigner.realigned_bam,
+      normal_realigned_bam_index=normal_Realigner.realigned_bam_index,
       normal_recal_table=normal_BQSR.recal_table,
-      tumor_recaled_bam=tumor_BQSR.recaled_bam,
-      tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
+      tumor_realigned_bam=tumor_Realigner.realigned_bam,
+      tumor_realigned_bam_index=tumor_Realigner.realigned_bam_index,
       tumor_recal_table=tumor_BQSR.recal_table,
       normal_name=sample_id + "_normal",
       tumor_name=sample_id + "_tumor",