Rename conflicting identifiers in CrossValidateGqRecalibrator.wdl

broadinstitute · Feb 26, 2024 · 3699b93 · 3699b93
1 parent 357efc1
commit 3699b93
Showing 1 changed file with 11 additions and 12 deletions.
diff --git a/wdl/CrossValidateGqRecalibrator.wdl b/wdl/CrossValidateGqRecalibrator.wdl
@@ -1,10 +1,9 @@
 version 1.0
 
-import "TrainGqRecalibrator.wdl" as TrainGqRecalibrator
-import "RecalibrateGq.wdl" as RecalibrateGq
-import "BenchmarkGqFilter.wdl" as BenchmarkGqFilter
-import "PickleVcfProperties.wdl" as PickleVcfProperties
-import "Utils.wdl" as Utils
+import "TrainGqRecalibrator.wdl" as train_recal
+import "RecalibrateGq.wdl" as recal_gq
+import "BenchmarkGqFilter.wdl" as bench_gq_filter
+import "PickleVcfProperties.wdl" as pickle
 
 workflow CrossValidateGqRecalibrator {
     input {
@@ -35,7 +34,7 @@ workflow CrossValidateGqRecalibrator {
         CrossValidationVcfs? pre_computed_cross_validation_vcfs
     }
 
-    call TrainGqRecalibrator.TrainGqRecalibrator {
+    call train_recal.TrainGqRecalibrator {
         input:
             train_vcf=train_vcf,
             train_vcf_index=train_vcf_index,
@@ -46,7 +45,7 @@ workflow CrossValidateGqRecalibrator {
             samtools_cloud_docker=samtools_cloud_docker
     }
 
-    call RecalibrateGq.RecalibrateGq as DirectGqRecalibrator {
+    call recal_gq.RecalibrateGq as DirectGqRecalibrator {
         input:
             vcf=train_vcf,
             vcf_index=train_vcf_index,
@@ -73,7 +72,7 @@ workflow CrossValidateGqRecalibrator {
                                                                pre_computed_cross_validation_vcfs])
 
     scatter(fold in range(length(cross_validation_vcfs_.train_vcfs))) {
-        call TrainGqRecalibrator.TrainGqRecalibrator as CrossTrainGqRecalibratorFold {
+        call train_recal.TrainGqRecalibrator as CrossTrainGqRecalibratorFold {
             input:
                 train_vcf=cross_validation_vcfs_.train_vcfs[fold],
                 train_vcf_index=cross_validation_vcfs_.train_vcf_indices[fold],
@@ -84,7 +83,7 @@ workflow CrossValidateGqRecalibrator {
                 samtools_cloud_docker=samtools_cloud_docker
         }
 
-        call RecalibrateGq.RecalibrateGq as CrossGqRecalibrator {
+        call recal_gq.RecalibrateGq as CrossGqRecalibrator {
             input:
                 vcf=cross_validation_vcfs_.test_vcfs[fold],
                 vcf_index=cross_validation_vcfs_.test_vcf_indices[fold],
@@ -108,7 +107,7 @@ workflow CrossValidateGqRecalibrator {
     # cromwell doesn't launch tasks until an entire workflow is ready, so can speed up wall-clock time by getting
     # variant properties and original scores as soon as train_vcf_ is resolved
     if(!defined(pre_computed_pickled_variant_properties)) {
-        call PickleVcfProperties.PickleVcfProperties as PickleVariantData {
+        call pickle.PickleVcfProperties as PickleVariantData {
             input:
                 vcf=train_vcf,
                 vcf_index=train_vcf_index,
@@ -121,7 +120,7 @@ workflow CrossValidateGqRecalibrator {
                                                      PickleVariantData.pickled_properties])
 
     if(!defined(pre_computed_pickled_original_scores)) {
-        call PickleVcfProperties.PickleVcfProperties as PickleTrainScores {
+        call pickle.PickleVcfProperties as PickleTrainScores {
             input:
                 vcf=train_vcf,
                 vcf_index=train_vcf_index,
@@ -161,7 +160,7 @@ workflow CrossValidateGqRecalibrator {
     Array[ScoresDataSet] comparison_scores_ = flatten([scores_0, comparison_scores])
 
     # actually call BenchmarkFilter workflow
-    call BenchmarkGqFilter.BenchmarkGqFilter {
+    call bench_gq_filter.BenchmarkGqFilter {
         input:
             data_label=train_vcf_label,
             original_scores=original_scores,