copy over the cromwell 52 changes to WARP (broadinstitute#70)

* copy over the cromwell 52 changes to WARP
kshakir · Sep 15, 2020 · df483cf · df483cf
1 parent 99297d3
commit df483cf
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diff --git a/pipelines/broad/annotation_filtration/AnnotationFiltration.changelog.md b/pipelines/broad/annotation_filtration/AnnotationFiltration.changelog.md
@@ -1,2 +1,7 @@
+# 1.1.0
+2020-08-18
+
+* Added a meta section with 'allowNestedInputs' set to 'true' to allow the workflow to use with nested inputs with Cromwell 52
+
 # 1.0
 Initial release of the AnnotationFiltration pipeline
diff --git a/pipelines/broad/annotation_filtration/AnnotationFiltration.wdl b/pipelines/broad/annotation_filtration/AnnotationFiltration.wdl
@@ -4,7 +4,7 @@ import "../../../tasks/broad/Funcotator.wdl" as Funcotator
 
 workflow AnnotationFiltration {
 
-  String pipeline_version = "1.0"
+  String pipeline_version = "1.1.0"
 
   input {
     Array[File] vcfs
@@ -86,6 +86,9 @@ workflow AnnotationFiltration {
     Array[File] significant_variant_vcfs = FilterFuncotations.significant_variants_vcf
     File filtration_report = GatherFiltrationReport.filtration_report
   }
+  meta {
+    allowNestedInputs: true
+  }
 }
 
 task FilterFuncotations {

diff --git a/pipelines/broad/arrays/multi_sample/MultiSampleArrays.changelog.md b/pipelines/broad/arrays/multi_sample/MultiSampleArrays.changelog.md
@@ -1,3 +1,8 @@
+# 1.5.0
+2020-08-18
+
+* Added a meta section with 'allowNestedInputs' set to 'true' to allow the workflow to use with nested inputs with Cromwell 52
+
 # 1.4
 2020-06-23
 

diff --git a/pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl b/pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl
@@ -18,7 +18,7 @@ version 1.0
 
 workflow MultiSampleArrays {
 
-  String pipeline_version = "1.4"
+  String pipeline_version = "1.5.0"
 
   input {
     File samples_fofn
@@ -63,6 +63,9 @@ workflow MultiSampleArrays {
     File combined_vcf = FinalCombine.combined_vcf
     File combined_vcf_index = FinalCombine.combined_vcf_index
   }
+  meta {
+    allowNestedInputs: true
+  }
 }
 
 

diff --git a/pipelines/broad/arrays/single_sample/Arrays.changelog.md b/pipelines/broad/arrays/single_sample/Arrays.changelog.md
@@ -1,3 +1,8 @@
+# 2.1.0
+2020-08-18
+
+* Added a meta section with 'allowNestedInputs' set to 'true' to allow the workflow to use with nested inputs with Cromwell 52
+
 # 2.0.1
 2020-08-31
 

diff --git a/pipelines/broad/arrays/single_sample/Arrays.wdl b/pipelines/broad/arrays/single_sample/Arrays.wdl
@@ -21,7 +21,7 @@ import "../../../../tasks/broad/InternalArraysTasks.wdl" as InternalTasks
 
 workflow Arrays {
 
-  String pipeline_version = "2.0.1"
+  String pipeline_version = "2.1.0"
 
   input {
 
@@ -272,4 +272,7 @@ workflow Arrays {
     File? GenotypeConcordanceDetailMetricsFile  = IlluminaGenotypingArray.genotype_concordance_detail_metrics
     File? GenotypeConcordanceContingencyMetricsFile = IlluminaGenotypingArray.genotype_concordance_contingency_metrics
   }
+  meta {
+    allowNestedInputs: true
+  }
 }
diff --git a/pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md b/pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md
@@ -1,3 +1,8 @@
+# 1.10.0
+2020-08-18
+
+* Added a meta section with 'allowNestedInputs' set to 'true' to allow the workflow to use with nested inputs with Cromwell 52
+
 # 1.9.1
 2020-08-31
 

diff --git a/pipelines/broad/arrays/validate_chip/ValidateChip.wdl b/pipelines/broad/arrays/validate_chip/ValidateChip.wdl
@@ -21,7 +21,7 @@ import "../../../../tasks/broad/InternalArraysTasks.wdl" as InternalTasks
 
 workflow ValidateChip {
 
-  String pipeline_version = "1.9.1"
+  String pipeline_version = "1.10.0"
 
   input {
     String sample_alias
@@ -244,6 +244,9 @@ workflow ValidateChip {
     File IndelGenotypeConcordanceVcfFile = IndelGenotypeConcordance.output_vcf
     File IndelGenotypeConcordanceTxtFile = IndelGenotypeConcordance.output_txt
   }
+  meta {
+    allowNestedInputs: true
+  }
 }
 
 

diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md
@@ -1,3 +1,8 @@
+# 1.2.1
+2020-08-28
+
+* Added 'allowNestedInputs: true' metadata parameter to wdl to support Cromwell version 48 and above
+
 # 1.2
 Joint Genotyping now accepts a flag to tell VariantRecalibrator to use non-allele-specific annotations. VCFs without allele-specific annotations can now be processed by providing `"JointGenotyping.use_allele_specific_annotations"` in the inputs JSON.
 

diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl
@@ -6,7 +6,7 @@ import "../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks
 # Joint Genotyping for hg38 Whole Genomes and Exomes (has not been tested on hg19)
 workflow JointGenotyping {
 
-  String pipeline_version = "1.2"
+  String pipeline_version = "1.2.1"
 
   input {
     File unpadded_intervals_file
@@ -453,4 +453,7 @@ workflow JointGenotyping {
     # Output the metrics from crosschecking fingerprints.
     File crosscheck_fingerprint_check = select_first([CrossCheckFingerprintSolo.crosscheck_metrics, GatherFingerprintingMetrics.gathered_metrics])
   }
+  meta {
+    allowNestedInputs: true
+  }
 }
diff --git a/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md b/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md
@@ -1,3 +1,8 @@
+# 1.2.1
+2020-08-28
+
+* Added 'allowNestedInputs: true' metadata parameter to wdl to support Cromwell version 48 and above
+
 # 1.2
 Joint Genotyping now accepts a flag to tell VariantRecalibrator to use non-allele-specific annotations. VCFs without allele-specific annotations can now be processed by providing `"JointGenotyping.use_allele_specific_annotations"` in the inputs JSON.
 

diff --git a/...ad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl b/...ad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl
@@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks
 # Joint Genotyping for hg38 Exomes and Whole Genomes (has not been tested on hg19)
 workflow JointGenotypingByChromosomePartOne {
 
-  String pipeline_version = "1.2"
+  String pipeline_version = "1.2.1"
 
   input {
     File unpadded_intervals_file
@@ -266,4 +266,7 @@ workflow JointGenotypingByChromosomePartOne {
     # Output the interval list generated/used by this run workflow.
     Array[File] output_intervals = SplitIntervalList.output_intervals
   }
+  meta {
+    allowNestedInputs: true
+  }
 }
diff --git a/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md b/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md
@@ -1,3 +1,8 @@
+# 1.2.1
+2020-08-28
+
+* Added 'allowNestedInputs: true' metadata parameter to wdl to support Cromwell version 48 and above
+
 # 1.2
 Joint Genotyping now accepts a flag to tell VariantRecalibrator to use non-allele-specific annotations. VCFs without allele-specific annotations can now be processed by providing `"JointGenotyping.use_allele_specific_annotations"` in the inputs JSON.
 

diff --git a/...ad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl b/...ad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl
@@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks
 # Joint Genotyping for hg38 Exomes and Whole Genomes (has not been tested on hg19)
 workflow JointGenotypingByChromosomePartTwo {
 
-  String pipeline_version = "1.2"
+  String pipeline_version = "1.2.1"
 
   input {
     String callset_name
@@ -223,5 +223,8 @@ workflow JointGenotypingByChromosomePartTwo {
 
     File crosscheck_metrics = GatherFingerprintingMetrics.gathered_metrics
   }
+  meta {
+    allowNestedInputs: true
+  }
 }
 
diff --git a/...nes/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md b/...nes/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md
@@ -1,2 +1,7 @@
+# 1.0.1
+2020-08-28
+
+* Added 'allowNestedInputs: true' metadata parameter to wdl to support Cromwell version 48 and above
+
 # 1.0
 Initial release of the ReblockGVCF pipeline. This is a WDL 1.0 version of the [workflow run in Terra](https://portal.firecloud.org/?return=terra#methods/methodsDev/ReblockGVCF-gatk4_exomes_goodCompression/4) for joint-genotyping projects. 
diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl
@@ -2,7 +2,7 @@ version 1.0
 
 workflow ReblockGVCF {
 
-  String pipeline_version = "1.0"
+  String pipeline_version = "1.0.1"
 
   input {
     File gvcf
@@ -24,6 +24,9 @@ workflow ReblockGVCF {
     File output_vcf = Reblock.output_vcf
     File output_vcf_index = Reblock.output_vcf_index
   }
+  meta {
+    allowNestedInputs: true
+  }
 }
 
 task Reblock {

diff --git a/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md b/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md
@@ -1,3 +1,8 @@
+# 2.1.0
+2020-08-18
+
+* Added 'allowNestedInputs: true' metadata parameter to wdl to support Cromwell version 52
+
 # 2.0.1
 2020-07-15
 

diff --git a/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl b/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl
@@ -39,7 +39,7 @@ import "../../../../../../structs/dna_seq/DNASeqStructs.wdl"
 # WORKFLOW DEFINITION
 workflow ExomeGermlineSingleSample {
 
-  String pipeline_version = "2.0.1"
+  String pipeline_version = "2.1.0"
 
   input {
     PapiSettings papi_settings
@@ -208,4 +208,7 @@ workflow ExomeGermlineSingleSample {
     File output_vcf = BamToGvcf.output_vcf
     File output_vcf_index = BamToGvcf.output_vcf_index
   }
+  meta {
+    allowNestedInputs: true
+  }
 }
diff --git a/...lines/broad/dna_seq/germline/single_sample/exome/test_inputs/Plumbing/RP-929.NA12878.json b/...lines/broad/dna_seq/germline/single_sample/exome/test_inputs/Plumbing/RP-929.NA12878.json
@@ -55,6 +55,9 @@
     "agg_preemptible_tries": 3
   },
 
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false,
+  "ExomeGermlineSingleSample.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true

diff --git a/...ad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/C1963.CHMI_CHMI3_Nex1.json b/...ad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/C1963.CHMI_CHMI3_Nex1.json
@@ -61,6 +61,8 @@
     "preemptible_tries": 3,
     "agg_preemptible_tries": 3
   },
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false
 }
diff --git a/...lines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/C862.NA19238.json b/...lines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/C862.NA19238.json
@@ -69,6 +69,8 @@
     "preemptible_tries": 3,
     "agg_preemptible_tries": 3
   },
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false
 }
diff --git a/...ines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12878.json b/...ines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12878.json
@@ -54,6 +54,8 @@
     "preemptible_tries": 3,
     "agg_preemptible_tries": 3
   },
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false
 }
diff --git a/...ines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12891.json b/...ines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12891.json
@@ -54,6 +54,8 @@
     "preemptible_tries": 3,
     "agg_preemptible_tries": 3
   },
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false
 }
diff --git a/...ines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12892.json b/...ines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12892.json
@@ -55,6 +55,8 @@
     "preemptible_tries": 3,
     "agg_preemptible_tries": 3
   },
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false
 }
diff --git a/...s/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/RP-1535.NA17-308.json b/...s/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/RP-1535.NA17-308.json
@@ -71,6 +71,8 @@
     "preemptible_tries": 3,
     "agg_preemptible_tries": 3
   },
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
+  "ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false,
   "ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false
 }
diff --git a/...dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md b/...dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md
@@ -1,3 +1,8 @@
+# 2.1.0
+2020-08-18
+
+* Added a meta section with 'allowNestedInputs' set to 'true' to allow the workflow to use with nested inputs with Cromwell 52
+
 # 2.0.1
 2020-07-15
 

diff --git a/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl b/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl
@@ -38,7 +38,7 @@ import "../../../../../../structs/dna_seq/DNASeqStructs.wdl"
 # WORKFLOW DEFINITION
 workflow WholeGenomeGermlineSingleSample {
 
-  String pipeline_version = "2.0.1"
+  String pipeline_version = "2.1.0"
 
   input {
     SampleAndUnmappedBams sample_and_unmapped_bams
@@ -218,4 +218,7 @@ workflow WholeGenomeGermlineSingleSample {
     File output_vcf = BamToGvcf.output_vcf
     File output_vcf_index = BamToGvcf.output_vcf_index
   }
+  meta {
+    allowNestedInputs: true
+  }
 }
diff --git a/pipelines/broad/dna_seq/germline/single_sample/wgs/test_inputs/Plumbing/G96830.NA12878.json b/pipelines/broad/dna_seq/germline/single_sample/wgs/test_inputs/Plumbing/G96830.NA12878.json
@@ -55,5 +55,6 @@
     "preemptible_tries": 3,
     "agg_preemptible_tries": 3
   },
+  "WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true,
   "WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true
 }
diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md
@@ -1,3 +1,8 @@
+# 1.10.0
+2020-08-18
+
+* Added a meta section with 'allowNestedInputs' set to 'true' to allow the workflow to use with nested inputs with Cromwell 52
+
 # 1.9
 2020-07-31
 

diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl
@@ -20,7 +20,7 @@ import "../../../../tasks/broad/IlluminaGenotypingArrayTasks.wdl" as GenotypingT
 
 workflow IlluminaGenotypingArray {
 
-  String pipeline_version = "1.9"
+  String pipeline_version = "1.10.0"
 
   input {
 
@@ -343,4 +343,7 @@ workflow IlluminaGenotypingArray {
     File? genotype_concordance_contingency_metrics = GenotypeConcordance.contingency_metrics
     Boolean? genotype_concordance_failed = GenotypeConcordance.fails_concordance
   }
+  meta {
+    allowNestedInputs: true
+  }
 }
diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 2.1.0
+2020-08-18
+
+* Added a meta section with 'allowNestedInputs' set to 'true' to allow the workflow to use with nested inputs with Cromwell 52
+
 # 2.0.2
 2020-07-31
 

diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.wdl b/pipelines/broad/reprocessing/exome/ExomeReprocessing.wdl
@@ -6,7 +6,7 @@ import "../../../../structs/dna_seq/DNASeqStructs.wdl"
 
 workflow ExomeReprocessing {
 
-  String pipeline_version = "2.0.2"
+  String pipeline_version = "2.1.0"
 
   input {
     File? input_cram
@@ -119,4 +119,7 @@ workflow ExomeReprocessing {
     File output_vcf = ExomeGermlineSingleSample.output_vcf
     File output_vcf_index = ExomeGermlineSingleSample.output_vcf_index
   }
+  meta {
+    allowNestedInputs: true
+  }
 }