Merge branch 'master' of github.com:TrinityCTAT/ctat-mutations

TrinityCTAT · Jun 29, 2024 · a092203 · a092203
2 parents c49380f + 2c44304
commit a092203
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diff --git a/WDL/Terra/ctat_mutations.Terra.hg19.wdl b/WDL/Terra/ctat_mutations.Terra.hg19.wdl
@@ -69,6 +69,7 @@ workflow ctat_mutations_Terra_hg19 {
         File? annotated_vcf = CM_Terra_wf.annotated_vcf
         File? filtered_vcf = CM_Terra_wf.filtered_vcf
         File? aligned_bam = CM_Terra_wf.aligned_bam
+        File? aligned_bai = CM_Terra_wf.aligned_bai
         File? output_log_final =  CM_Terra_wf.output_log_final
         File? output_SJ =  CM_Terra_wf.output_SJ
         File? recalibrated_bam = CM_Terra_wf.recalibrated_bam

diff --git a/WDL/Terra/ctat_mutations.Terra.hg38.wdl b/WDL/Terra/ctat_mutations.Terra.hg38.wdl
@@ -76,6 +76,7 @@ workflow ctat_mutations_Terra_hg38 {
         File? annotated_vcf = CM_Terra_wf.annotated_vcf
         File? filtered_vcf = CM_Terra_wf.filtered_vcf
         File? aligned_bam = CM_Terra_wf.aligned_bam
+        File? aligned_bai = CM_Terra_wf.aligned_bai
         File? output_log_final =  CM_Terra_wf.output_log_final
         File? output_SJ =  CM_Terra_wf.output_SJ
         File? recalibrated_bam = CM_Terra_wf.recalibrated_bam

diff --git a/WDL/Terra/ctat_mutations.Terra.wdl b/WDL/Terra/ctat_mutations.Terra.wdl
@@ -105,6 +105,7 @@ workflow ctat_mutations_Terra {
         File? annotated_vcf = CM_wf.annotated_vcf
         File? filtered_vcf = CM_wf.filtered_vcf
         File? aligned_bam = CM_wf.aligned_bam
+        File? aligned_bai = CM_wf.aligned_bai
         File? output_log_final =  CM_wf.output_log_final
         File? output_SJ =  CM_wf.output_SJ
         File? recalibrated_bam = CM_wf.recalibrated_bam

diff --git a/WDL/ctat_mutations.wdl b/WDL/ctat_mutations.wdl
@@ -615,6 +615,7 @@ workflow ctat_mutations {
         File? annotated_vcf = AnnotateVariants.vcf
         File? filtered_vcf = VariantFiltration.vcf
         File? aligned_bam = StarAlign.bam
+        File? aligned_bai = StarAlign.bai
         File? output_log_final =  StarAlign.output_log_final
         File? output_SJ =  StarAlign.output_SJ
         File? recalibrated_bam = ApplyBQSR.bam