Fix bug: TNscope.wdl

tasks/Dedup.wdl

@@ -29,8 +29,8 @@ task Dedup {
   output {
     File score = "${sample}_score.txt"
     File dedup_metrics = "${sample}_dedup_metrics.txt"
-    File Dedup_bam = "${sample}.sorted.deduped.bam"
-    File Dedup_bam_index = "${sample}.sorted.deduped.bam.bai"
+    File deduped_bam = "${sample}.sorted.deduped.bam"
+    File deduped_bam_index = "${sample}.sorted.deduped.bam.bai"
   }
 }
 

tasks/Realigner.wdl

@@ -8,8 +8,8 @@ task Realigner {
   String sample
   String fasta
 
-  File Dedup_bam
-  File Dedup_bam_index
+  File deduped_bam
+  File deduped_bam_index
   String db_mills
   String docker
   String cluster_config
@@ -23,7 +23,7 @@ task Realigner {
     
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
     -r ${ref_dir}/${fasta} \
-    -i ${Dedup_bam} \
+    -i ${deduped_bam} \
     --algo Realigner -k ${dbmills_dir}/${db_mills} ${sample}.sorted.deduped.realigned.bam
     
   >>>

tasks/TNscope.wdl

@@ -3,11 +3,11 @@ task TNscope {
   String sample
   String SENTIEON_INSTALL_DIR
   String SENTIEON_LICENSE
-  File tumor_recaled_bam
-  File tumor_recaled_bam_index
+  File tumor_deduped_bam
+  File tumor_deduped_bam_index
   File tumor_recal_table
-  File normal_recaled_bam
-  File normal_recaled_bam_index
+  File normal_deduped_bam
+  File normal_deduped_bam_index
   File normal_recal_table
   String tumor_name
   String normal_name
@@ -45,8 +45,8 @@ task TNscope {
 
     ${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_deduped_bam} -q ${tumor_recal_table} \
+    -i ${normal_deduped_bam} -q ${normal_recal_table} \
     --algo TNscope \
     --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
     --dbsnp ${dbsnp_dir}/${dbsnp} \

tasks/deduped_Metrics.wdl

@@ -5,8 +5,8 @@ task deduped_Metrics {
   String SENTIEON_LICENSE
   String sample
   String fasta
-  File Dedup_bam
-  File Dedup_bam_index
+  File deduped_bam
+  File deduped_bam_index
   String docker
   String cluster_config
   String disk_size
@@ -27,7 +27,7 @@ task deduped_Metrics {
 
     ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
     -r ${ref_dir}/${fasta} $INTERVAL \
-    -i ${Dedup_bam} \
+    -i ${deduped_bam} \
     --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics \
     --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt \
     --algo QualDistribution ${sample}_deduped_qd_metrics.txt \

workflow.wdl

@@ -99,8 +99,8 @@ workflow {{ project_name }} {
       SENTIEON_LICENSE=SENTIEON_LICENSE,
       fasta=fasta,
       ref_dir=ref_dir,
-      Dedup_bam=tumor_Dedup.Dedup_bam,
-      Dedup_bam_index=tumor_Dedup.Dedup_bam_index,
+      deduped_bam=tumor_Dedup.deduped_bam,
+      deduped_bam_index=tumor_Dedup.deduped_bam_index,
       sample=sample_id + '_tumor',
       docker=sentieon_docker,
       disk_size=disk_size,
@@ -113,8 +113,8 @@ workflow {{ project_name }} {
       SENTIEON_LICENSE=SENTIEON_LICENSE,
       fasta=fasta,
       ref_dir=ref_dir,
-      Dedup_bam=tumor_Dedup.Dedup_bam,
-      Dedup_bam_index=tumor_Dedup.Dedup_bam_index,
+      deduped_bam=tumor_Dedup.deduped_bam,
+      deduped_bam_index=tumor_Dedup.deduped_bam_index,
       db_mills=db_mills,
       dbmills_dir=dbmills_dir,
       sample=sample_id + '_tumor',
@@ -191,8 +191,8 @@ workflow {{ project_name }} {
     SENTIEON_LICENSE=SENTIEON_LICENSE,
     fasta=fasta,
     ref_dir=ref_dir,
-    Dedup_bam=normal_Dedup.Dedup_bam,
-    Dedup_bam_index=normal_Dedup.Dedup_bam_index,
+    deduped_bam=normal_Dedup.deduped_bam,
+    deduped_bam_index=normal_Dedup.deduped_bam_index,
     sample=sample_id + '_normal',
     regions=regions,
     docker=sentieon_docker,
@@ -206,8 +206,8 @@ workflow {{ project_name }} {
     SENTIEON_LICENSE=SENTIEON_LICENSE,
     fasta=fasta,
     ref_dir=ref_dir,
-    Dedup_bam=normal_Dedup.Dedup_bam,
-    Dedup_bam_index=normal_Dedup.Dedup_bam_index,
+    deduped_bam=normal_Dedup.deduped_bam,
+    deduped_bam_index=normal_Dedup.deduped_bam_index,
     db_mills=db_mills,
     dbmills_dir=dbmills_dir,
     sample=sample_id + '_normal',
@@ -297,11 +297,11 @@ 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_deduped_bam=normal_Dedup.deduped_bam,
+      normal_deduped_bam_index=normal_Dedup.deduped_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_deduped_bam=tumor_Dedup.deduped_bam,
+      tumor_deduped_bam_index=tumor_Dedup.deduped_bam_index,
       tumor_recal_table=tumor_BQSR.recal_table,
       normal_name=sample_id + "_normal",
       tumor_name=sample_id + "_tumor",