Rewrote imports for release v0.2-test for Dockstore

broadinstitute · Dec 3, 2019 · e4f4deb · e4f4deb
1 parent 6963d4c
commit e4f4deb
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Showing 98 changed files with 195 additions and 195 deletions.
diff --git a/ClinicalFiltering.wdl b/ClinicalFiltering.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/Structs.wdl"
 
 task FilterVcfBySampleGenotypeAndAddEvidenceAnnotation {
   input {

diff --git a/GATKSVPipelineClinical.wdl b/GATKSVPipelineClinical.wdl
@@ -1,20 +1,20 @@
 version 1.0
 
-import "module00a/Module00a.wdl" as m00a
-import "module00b/Module00b.wdl" as m00b
-import "module00b/PloidyEstimation.wdl" as pe
-import "module00c/Module00c.wdl" as m00c
-import "module00c/DepthPreprocessing.wdl" as dpn
-import "module01/Module01.wdl" as m01
-import "module02/Module02.wdl" as m02
-import "module02/SRTest.wdl" as SRTest
-import "module03/Module03.wdl" as m03
-import "module04/Module04.wdl" as m04
-import "module05_06/Module05_06.wdl" as m0506
-import "gcnv/GermlineCNVCase.wdl" as gcnv
-import "ClinicalFiltering.wdl" as ClinicalFiltering
-import "GATKSVPipelineClinicalMetrics.wdl" as ClinicalMetrics
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Module00a.wdl" as m00a
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00b/Module00b.wdl" as m00b
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00b/PloidyEstimation.wdl" as pe
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00c/Module00c.wdl" as m00c
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00c/DepthPreprocessing.wdl" as dpn
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module01/Module01.wdl" as m01
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module02/Module02.wdl" as m02
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module02/SRTest.wdl" as SRTest
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module03/Module03.wdl" as m03
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module04/Module04.wdl" as m04
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module05_06/Module05_06.wdl" as m0506
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/gcnv/GermlineCNVCase.wdl" as gcnv
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/ClinicalFiltering.wdl" as ClinicalFiltering
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/GATKSVPipelineClinicalMetrics.wdl" as ClinicalMetrics
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/Structs.wdl"
 
 # GATK SV Pipeline single sample mode
 # Runs Modules 00abc, 01, 03.MergePesrVcfs, 04, 05/06

diff --git a/GATKSVPipelineClinicalMetrics.wdl b/GATKSVPipelineClinicalMetrics.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "TestUtils.wdl" as tu
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/TestUtils.wdl" as tu
 
 workflow ClinicalMetrics {
   input {

diff --git a/GATKSVPipelineClinicalTest.wdl b/GATKSVPipelineClinicalTest.wdl
@@ -1,7 +1,7 @@
 version 1.0
 
-import "GATKSVPipelineClinical.wdl" as module
-import "TestUtils.wdl" as utils
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/GATKSVPipelineClinical.wdl" as module
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/TestUtils.wdl" as utils
 
 workflow GATKSVPipelineClinicalTest {
   input {

diff --git a/TestUtils.wdl b/TestUtils.wdl
@@ -538,4 +538,4 @@ task PlotMetrics {
     maxRetries: 1
   }
 
-}
+}
diff --git a/gcnv/CollectCoverage.wdl b/gcnv/CollectCoverage.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/gcnv/Structs.wdl"
 
 workflow CollectCoverage {
 
@@ -297,4 +297,4 @@ task CountsToIntervals {
   output {
     File out = "~{output_name}.interval_list"
   }
-}
+}
diff --git a/gcnv/CramToBam.wdl b/gcnv/CramToBam.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/gcnv/Structs.wdl"
 
 workflow CramToBam {
   input {
@@ -189,4 +189,4 @@ task RunCramToBamRequesterPays {
     maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
   }
 
-}
+}
diff --git a/gcnv/GermlineCNVCase.wdl b/gcnv/GermlineCNVCase.wdl
@@ -23,7 +23,7 @@
 
 version 1.0
 
-import "GermlineCNVTasks.wdl" as CNVTasks
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/gcnv/GermlineCNVTasks.wdl" as CNVTasks
 
 workflow CNVGermlineCaseWorkflow {
 

diff --git a/gcnv/GermlineCNVCohort.wdl b/gcnv/GermlineCNVCohort.wdl
@@ -4,7 +4,7 @@
 
 version 1.0
 
-import "GermlineCNVTasks.wdl" as CNVTasks
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/gcnv/GermlineCNVTasks.wdl" as CNVTasks
 
 workflow CNVGermlineCohortWorkflow {
     input {

diff --git a/gcnv/trainGCNV.wdl b/gcnv/trainGCNV.wdl
@@ -1,9 +1,9 @@
 version 1.0
 
-import "Structs.wdl"
-import "CollectCoverage.wdl" as cov
-import "CramToBam.wdl" as ctb
-import "GermlineCNVCohort.wdl" as gcnv_cohort
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/gcnv/Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/gcnv/CollectCoverage.wdl" as cov
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/gcnv/CramToBam.wdl" as ctb
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/gcnv/GermlineCNVCohort.wdl" as gcnv_cohort
 
 # Trains gCNV model on a cohort with counts already collected
 workflow TrainGCNV {

diff --git a/module00a/BAF.wdl b/module00a/BAF.wdl
@@ -10,7 +10,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Structs.wdl"
 
 workflow BAF {
   input {
@@ -428,4 +428,4 @@ task ScatterBAFBySample {
     preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
     maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
   }
-}
+}
diff --git a/module00a/CollectCoverage.wdl b/module00a/CollectCoverage.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Structs.wdl"
 
 workflow CollectCoverage {
 
@@ -297,4 +297,4 @@ task CountsToIntervals {
   output {
     File out = "~{output_name}.interval_list"
   }
-}
+}
diff --git a/module00a/CramToBam.wdl b/module00a/CramToBam.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Structs.wdl"
 
 workflow CramToBam {
   input {
@@ -189,4 +189,4 @@ task RunCramToBamRequesterPays {
     maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
   }
 
-}
+}
diff --git a/module00a/Delly.wdl b/module00a/Delly.wdl
@@ -23,7 +23,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Structs.wdl"
 
 workflow Delly {
   # Run Delly SV detection algorithm on whole genomes in array of

diff --git a/module00a/Manta.wdl b/module00a/Manta.wdl
@@ -23,7 +23,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Structs.wdl"
 
 workflow Manta {
   input {

diff --git a/module00a/Module00a.wdl b/module00a/Module00a.wdl
@@ -6,14 +6,14 @@
 
 version 1.0
 
-import "Structs.wdl"
-import "BAF.wdl" as baf
-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/v0.2-test/module00a/Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/BAF.wdl" as baf
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/CollectCoverage.wdl" as cov
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/CramToBam.wdl" as ctb
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Delly.wdl" as delly
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Manta.wdl" as manta
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/PESRCollection.wdl" as pesr
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Whamg.wdl" as wham
 
 # Runs selected tools on BAM/CRAM files
 
@@ -313,4 +313,4 @@ task DeleteIntermediateFiles {
     preemptible: "3"
     maxRetries: "1"
   }
-}
+}
diff --git a/module00a/Module00aMetrics.wdl b/module00a/Module00aMetrics.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "TestUtils.wdl" as tu
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/TestUtils.wdl" as tu
 
 workflow Module00aMetrics {
   input {

diff --git a/module00a/Module00aTest.wdl b/module00a/Module00aTest.wdl
@@ -1,8 +1,8 @@
 version 1.0
 
-import "Module00a.wdl" as module
-import "Module00aMetrics.wdl" as metrics
-import "TestUtils.wdl" as utils
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Module00a.wdl" as module
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Module00aMetrics.wdl" as metrics
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/TestUtils.wdl" as utils
 
 workflow Module00aTest {
   input {

diff --git a/module00a/PESRCollection.wdl b/module00a/PESRCollection.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Structs.wdl"
 
 # Workflow to run PE/SR collection on a single sample
 workflow PESRCollection {

diff --git a/module00a/TestUtils.wdl b/module00a/TestUtils.wdl
@@ -538,4 +538,4 @@ task PlotMetrics {
     maxRetries: 1
   }
 
-}
+}
diff --git a/module00a/Whamg.wdl b/module00a/Whamg.wdl
@@ -1,7 +1,7 @@
 version 1.0
 
-import "Structs.wdl"
-import "CramToBam.wdl" as ctb
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00a/CramToBam.wdl" as ctb
 
 # Run Whamg SV detection algorithm on whole genome in bam or cram
 #   file, or if whitelist is provided, run whamg on whitelisted

diff --git a/module00b/BincovQC.wdl b/module00b/BincovQC.wdl
@@ -23,7 +23,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00b/Structs.wdl"
 
 # Workflow to run binCov QC on a single sample
 workflow BincovQC {

diff --git a/module00b/MakeBincovMatrix.wdl b/module00b/MakeBincovMatrix.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00b/Structs.wdl"
 
 workflow BincovMatrix {
   input {

diff --git a/module00b/Module00b.wdl b/module00b/Module00b.wdl
@@ -6,11 +6,11 @@ version 1.0
 
 ##########################################################################################
 
-import "Structs.wdl"
-import "MakeBincovMatrix.wdl" as mbm
-import "PloidyEstimation.wdl" as pe
-import "RawVcfQC.wdl" as vcfqc
-import "WGD.wdl" as wgd
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00b/Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00b/MakeBincovMatrix.wdl" as mbm
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00b/PloidyEstimation.wdl" as pe
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00b/RawVcfQC.wdl" as vcfqc
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00b/WGD.wdl" as wgd
 
 # Runs single sample tasks on collected evidence:
 #   - Ploidy determination

diff --git a/module00b/PloidyEstimation.wdl b/module00b/PloidyEstimation.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00b/Structs.wdl"
 
 workflow Ploidy {
   input {

diff --git a/module00b/RawVcfQC.wdl b/module00b/RawVcfQC.wdl
@@ -25,7 +25,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00b/Structs.wdl"
 
 workflow RawVcfQC {
   input {

diff --git a/module00b/WGD.wdl b/module00b/WGD.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00b/Structs.wdl"
 
 workflow WGD {
   input {

diff --git a/module00c/BatchEvidenceMerging.wdl b/module00c/BatchEvidenceMerging.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00c/Structs.wdl"
 
 workflow EvidenceMerging {
   input {

diff --git a/module00c/CNMOPS.wdl b/module00c/CNMOPS.wdl
@@ -8,7 +8,7 @@ version 1.0
 
 ##########################################################################################
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00c/Structs.wdl"
 
 ## cnMOPS worflow definition ##
 ## mode = sex (1=male, 2=female)

diff --git a/module00c/CollectCoverage.wdl b/module00c/CollectCoverage.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00c/Structs.wdl"
 
 workflow CollectCoverage {
 
@@ -297,4 +297,4 @@ task CountsToIntervals {
   output {
     File out = "~{output_name}.interval_list"
   }
-}
+}
diff --git a/module00c/DepthPreprocessing.wdl b/module00c/DepthPreprocessing.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00c/Structs.wdl"
 
 workflow MergeDepth {
   input {

diff --git a/module00c/GermlineCNVCase.wdl b/module00c/GermlineCNVCase.wdl
@@ -23,7 +23,7 @@
 
 version 1.0
 
-import "GermlineCNVTasks.wdl" as CNVTasks
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00c/GermlineCNVTasks.wdl" as CNVTasks
 
 workflow CNVGermlineCaseWorkflow {
 

diff --git a/module00c/MakeBincovMatrix.wdl b/module00c/MakeBincovMatrix.wdl
@@ -8,7 +8,7 @@
 
 version 1.0
 
-import "Structs.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/gatk-sv-clinical/v0.2-test/module00c/Structs.wdl"
 
 workflow BincovMatrix {
   input {
-Original file line number
+Diff line change
@@ Expand Up / @@ -538,4 +538,4 @@ task PlotMetrics { @@
         maxRetries: 1
       }
-    }
+    }