Rewrote imports for release v0.7.1 for Dockstore

broadinstitute · May 1, 2020 · ed40e0e · ed40e0e
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commit ed40e0e
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diff --git a/wdl/03_qc.wdl b/wdl/03_qc.wdl
@@ -6,7 +6,7 @@
 
 ##########################################################################################
 
-import "master_vcf_qc.wdl" as vcf_qc
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/master_vcf_qc.wdl" as vcf_qc
 
 workflow variant_filtering_qc {
 

diff --git a/wdl/BAFFromGVCFs.wdl b/wdl/BAFFromGVCFs.wdl
@@ -10,7 +10,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow BAFFromGVCFs {
   input {

diff --git a/wdl/BAFFromShardedVCF.wdl b/wdl/BAFFromShardedVCF.wdl
@@ -8,8 +8,8 @@
 
 version 1.0
 
-import "BAFFromGVCFs.wdl" as baf
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/BAFFromGVCFs.wdl" as baf
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow BAFFromShardedVCF {
   input {

diff --git a/wdl/BAFTest.wdl b/wdl/BAFTest.wdl
@@ -8,8 +8,8 @@
 
 version 1.0
 
-import "Tasks02.wdl" as tasks02
-import "BAFTestChromosome.wdl" as bafc
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Tasks02.wdl" as tasks02
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/BAFTestChromosome.wdl" as bafc
 
 workflow BAFTest {
 

diff --git a/wdl/BAFTestChromosome.wdl b/wdl/BAFTestChromosome.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow BAFTestChromosome {
   input {

diff --git a/wdl/BatchEvidenceMerging.wdl b/wdl/BatchEvidenceMerging.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow EvidenceMerging {
   input {

diff --git a/wdl/CNMOPS.wdl b/wdl/CNMOPS.wdl
@@ -8,7 +8,7 @@ version 1.0
 
 ##########################################################################################
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 ## cnMOPS worflow definition ##
 ## mode = sex (1=male, 2=female)

diff --git a/wdl/CleanVcf.wdl b/wdl/CleanVcf.wdl
@@ -6,8 +6,8 @@ version 1.0
 # based on snapshot 20
 # https://portal.firecloud.org/#methods/Talkowski-SV/05_CleanVCF3/20/wdl
 
-import "Structs.wdl"
-import "Tasks0506.wdl" as MiniTasks
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Tasks0506.wdl" as MiniTasks
 
 workflow CleanVcf {
   input {

diff --git a/wdl/ClusterSingleChromosome.wdl b/wdl/ClusterSingleChromosome.wdl
@@ -8,8 +8,8 @@ version 1.0
 
 # Distributed under terms of the MIT License
 
-import "Tasks0506.wdl" as MiniTasks
-import "ShardedCluster.wdl" as ShardedCluster
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Tasks0506.wdl" as MiniTasks
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/ShardedCluster.wdl" as ShardedCluster
 
 # Workflow to perform sharding & clustering of a vcf for a single chromosome
 workflow ClusterSingleChrom {

diff --git a/wdl/CollectCoverage.wdl b/wdl/CollectCoverage.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow CollectCoverage {
 

diff --git a/wdl/CombineReassess.wdl b/wdl/CombineReassess.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow CombineReassess {
   input {

diff --git a/wdl/CombineRegeno.wdl b/wdl/CombineRegeno.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow MergeCohortVcfs {
   input {

diff --git a/wdl/CramToBam.wdl b/wdl/CramToBam.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow CramToBam {
   input {

diff --git a/wdl/Delly.wdl b/wdl/Delly.wdl
@@ -23,7 +23,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow Delly {
   # Run Delly SV detection algorithm on whole genomes in array of

diff --git a/wdl/DepthClustering.wdl b/wdl/DepthClustering.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow ClusterDepth {
   input {

diff --git a/wdl/DepthPreprocessing.wdl b/wdl/DepthPreprocessing.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow MergeDepth {
   input {

diff --git a/wdl/FilterOutliers.wdl b/wdl/FilterOutliers.wdl
@@ -14,7 +14,7 @@ version 1.0
 
 # Distributed under terms of the MIT License
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 # Workflow to identify & filter outliers from VCFs after module 03 (random forest)
 workflow FilterOutlierSamples {

diff --git a/wdl/GATKSVPipelineSingleSample.wdl b/wdl/GATKSVPipelineSingleSample.wdl
@@ -1,21 +1,21 @@
 version 1.0
 
-import "Module00a.wdl" as m00a
-import "Module00b.wdl" as m00b
-import "PloidyEstimation.wdl" as pe
-import "Module00c.wdl" as m00c
-import "DepthPreprocessing.wdl" as dpn
-import "Module01.wdl" as m01
-import "Module02.wdl" as m02
-import "SRTest.wdl" as SRTest
-import "Module03.wdl" as m03
-import "Module04.wdl" as m04
-import "Module05_06.wdl" as m0506
-import "GermlineCNVCase.wdl" as gcnv
-import "SingleSampleFiltering.wdl" as SingleSampleFiltering
-import "GATKSVPipelineSingleSampleMetrics.wdl" as SingleSampleMetrics
-import "Utils.wdl" as utils
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Module00a.wdl" as m00a
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Module00b.wdl" as m00b
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/PloidyEstimation.wdl" as pe
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Module00c.wdl" as m00c
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/DepthPreprocessing.wdl" as dpn
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Module01.wdl" as m01
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Module02.wdl" as m02
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/SRTest.wdl" as SRTest
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Module03.wdl" as m03
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Module04.wdl" as m04
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Module05_06.wdl" as m0506
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/GermlineCNVCase.wdl" as gcnv
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/SingleSampleFiltering.wdl" as SingleSampleFiltering
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/GATKSVPipelineSingleSampleMetrics.wdl" as SingleSampleMetrics
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Utils.wdl" as utils
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 # GATK SV Pipeline single sample mode
 # Runs Modules 00abc, 01, 03.MergePesrVcfs, 04, 05/06

diff --git a/wdl/GATKSVPipelineSingleSampleMetrics.wdl b/wdl/GATKSVPipelineSingleSampleMetrics.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "TestUtils.wdl" as tu
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/TestUtils.wdl" as tu
 
 workflow SingleSampleMetrics {
   input {

diff --git a/wdl/GATKSVPipelineSingleSampleTest.wdl b/wdl/GATKSVPipelineSingleSampleTest.wdl
@@ -1,7 +1,7 @@
 version 1.0
 
-import "GATKSVPipelineSingleSample.wdl" as module
-import "TestUtils.wdl" as utils
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/GATKSVPipelineSingleSample.wdl" as module
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/TestUtils.wdl" as utils
 
 workflow GATKSVPipelineSingleSampleTest {
   input {

diff --git a/wdl/GenotypeCpxCnvs.wdl b/wdl/GenotypeCpxCnvs.wdl
@@ -8,8 +8,8 @@ version 1.0
 
 # Distributed under terms of the MIT License
 
-import "GenotypeCpxCnvsPerBatch.wdl" as RunDepthGenotypePerBatch
-import "Tasks0506.wdl" as MiniTasks
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/GenotypeCpxCnvsPerBatch.wdl" as RunDepthGenotypePerBatch
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Tasks0506.wdl" as MiniTasks
 
 # Workflow to perform depth-based genotyping for a single vcf shard scattered
 # across batches on predicted CPX CNVs from 04b

diff --git a/wdl/GenotypeCpxCnvsPerBatch.wdl b/wdl/GenotypeCpxCnvsPerBatch.wdl
@@ -9,7 +9,7 @@ version 1.0
 
 # Distributed under terms of the MIT License
 
-import "Tasks0506.wdl" as MiniTasks
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Tasks0506.wdl" as MiniTasks
 
 # Workflow to perform depth-based genotyping per batch
 # on predicted CPX CNVs from 04b

diff --git a/wdl/GenotypeDepthPart1.wdl b/wdl/GenotypeDepthPart1.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "TrainRDGenotyping.wdl" as rd_train
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/TrainRDGenotyping.wdl" as rd_train
 
 workflow GenotypeDepthPart1 {
   input {

diff --git a/wdl/GenotypeDepthPart2.wdl b/wdl/GenotypeDepthPart2.wdl
@@ -8,8 +8,8 @@
 
 version 1.0
 
-import "Structs.wdl"
-import "Tasks04.wdl" as tasks04
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Tasks04.wdl" as tasks04
 
 workflow GenotypeDepthPart2 {
   input {

diff --git a/wdl/GenotypePESRPart1.wdl b/wdl/GenotypePESRPart1.wdl
@@ -8,9 +8,9 @@
 
 version 1.0
 
-import "TrainRDGenotyping.wdl" as rd_train
-import "TrainPEGenotyping.wdl" as pe_train
-import "TrainSRGenotyping.wdl" as sr_train
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/TrainRDGenotyping.wdl" as rd_train
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/TrainPEGenotyping.wdl" as pe_train
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/TrainSRGenotyping.wdl" as sr_train
 
 workflow GenotypePESRPart1 {
   input {

diff --git a/wdl/GenotypePESRPart2.wdl b/wdl/GenotypePESRPart2.wdl
@@ -8,8 +8,8 @@
 
 version 1.0
 
-import "Structs.wdl"
-import "Tasks04.wdl" as tasks04
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Tasks04.wdl" as tasks04
 
 workflow GenotypePESRPart2 {
   input {

diff --git a/wdl/Genotype_2.wdl b/wdl/Genotype_2.wdl
@@ -1,5 +1,5 @@
 version 1.0
-import "Tasks04.wdl" as task04
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Tasks04.wdl" as task04
 
 workflow Regenotype{
   input{

diff --git a/wdl/Genotype_3.wdl b/wdl/Genotype_3.wdl
@@ -1,5 +1,5 @@
 version 1.0
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 workflow Regeno{
   input{
   File depth_vcf

diff --git a/wdl/GermlineCNVCase.wdl b/wdl/GermlineCNVCase.wdl
@@ -23,7 +23,7 @@
 
 version 1.0
 
-import "GermlineCNVTasks.wdl" as CNVTasks
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/GermlineCNVTasks.wdl" as CNVTasks
 
 workflow CNVGermlineCaseWorkflow {
 

diff --git a/wdl/GermlineCNVCohort.wdl b/wdl/GermlineCNVCohort.wdl
@@ -4,7 +4,7 @@
 
 version 1.0
 
-import "GermlineCNVTasks.wdl" as CNVTasks
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/GermlineCNVTasks.wdl" as CNVTasks
 
 workflow CNVGermlineCohortWorkflow {
     input {

diff --git a/wdl/GermlineCNVTasks.wdl b/wdl/GermlineCNVTasks.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 task AnnotateIntervals {
     input {

diff --git a/wdl/MakeBincovMatrix.wdl b/wdl/MakeBincovMatrix.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow BincovMatrix {
   input {

diff --git a/wdl/Manta.wdl b/wdl/Manta.wdl
@@ -23,7 +23,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow Manta {
   input {

diff --git a/wdl/MatrixQC.wdl b/wdl/MatrixQC.wdl
@@ -22,7 +22,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow MatrixQC {
   input {

diff --git a/wdl/MedianCov.wdl b/wdl/MedianCov.wdl
@@ -10,7 +10,7 @@ version 1.0
 
 # Workflow definition for Calculating Median Coverage 
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow MedianCov {
   input {

diff --git a/wdl/MergeCohortVcfs.wdl b/wdl/MergeCohortVcfs.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
 
 workflow MergeCohortVcfs {
   input {

diff --git a/wdl/Module00a.wdl b/wdl/Module00a.wdl
@@ -6,15 +6,15 @@
 
 version 1.0
 
-import "Structs.wdl"
-import "BAFFromGVCFs.wdl" as baf
-import "BAFFromShardedVCF.wdl" as sbaf
-import "CollectCoverage.wdl" as cov
-import "CramToBam.wdl" as ctb
-import "Delly.wdl" as delly
-import "Manta.wdl" as manta
-import "PESRCollection.wdl" as pesr
-import "Whamg.wdl" as wham
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/BAFFromGVCFs.wdl" as baf
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/BAFFromShardedVCF.wdl" as sbaf
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/CollectCoverage.wdl" as cov
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/CramToBam.wdl" as ctb
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Delly.wdl" as delly
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Manta.wdl" as manta
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/PESRCollection.wdl" as pesr
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/Whamg.wdl" as wham
 
 # Runs selected tools on BAM/CRAM files
 

diff --git a/wdl/Module00aMetrics.wdl b/wdl/Module00aMetrics.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "TestUtils.wdl" as tu
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.7.1/wdl/TestUtils.wdl" as tu
 
 workflow Module00aMetrics {
   input {