diff --git a/wdl/CrossValidateGqRecalibrator.wdl b/wdl/CrossValidateGqRecalibrator.wdl index e93260629..268d36954 100644 --- 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,