From df483cf53217606435bde50834a74073b5feb284 Mon Sep 17 00:00:00 2001 From: Sophie Crennan <48878747+sophiacrennan@users.noreply.github.com> Date: Tue, 15 Sep 2020 12:56:22 -0400 Subject: [PATCH] copy over the cromwell 52 changes to WARP (#70) * copy over the cromwell 52 changes to WARP --- .../AnnotationFiltration.changelog.md | 5 +++ .../AnnotationFiltration.wdl | 5 ++- .../MultiSampleArrays.changelog.md | 5 +++ .../arrays/multi_sample/MultiSampleArrays.wdl | 5 ++- .../arrays/single_sample/Arrays.changelog.md | 5 +++ .../broad/arrays/single_sample/Arrays.wdl | 5 ++- .../validate_chip/ValidateChip.changelog.md | 5 +++ .../arrays/validate_chip/ValidateChip.wdl | 5 ++- .../JointGenotyping.changelog.md | 5 +++ .../joint_genotyping/JointGenotyping.wdl | 5 ++- ...GenotypingByChromosomePartOne.changelog.md | 5 +++ .../JointGenotypingByChromosomePartOne.wdl | 5 ++- ...GenotypingByChromosomePartTwo.changelog.md | 5 +++ .../JointGenotypingByChromosomePartTwo.wdl | 5 ++- .../reblocking/ReblockGVCF.changelog.md | 5 +++ .../reblocking/ReblockGVCF.wdl | 5 ++- .../ExomeGermlineSingleSample.changelog.md | 5 +++ .../exome/ExomeGermlineSingleSample.wdl | 5 ++- .../test_inputs/Plumbing/RP-929.NA12878.json | 3 ++ .../Scientific/C1963.CHMI_CHMI3_Nex1.json | 2 ++ .../test_inputs/Scientific/C862.NA19238.json | 2 ++ .../test_inputs/Scientific/D5327.NA12878.json | 2 ++ .../test_inputs/Scientific/D5327.NA12891.json | 2 ++ .../test_inputs/Scientific/D5327.NA12892.json | 2 ++ .../Scientific/RP-1535.NA17-308.json | 2 ++ ...oleGenomeGermlineSingleSample.changelog.md | 5 +++ .../wgs/WholeGenomeGermlineSingleSample.wdl | 5 ++- .../test_inputs/Plumbing/G96830.NA12878.json | 1 + .../IlluminaGenotypingArray.changelog.md | 5 +++ .../illumina/IlluminaGenotypingArray.wdl | 5 ++- .../exome/ExomeReprocessing.changelog.md | 5 +++ .../reprocessing/exome/ExomeReprocessing.wdl | 5 ++- .../test_inputs/Plumbing/RP-929.NA12878.json | 3 ++ .../Scientific/C1963.CHMI_CHMI3_Nex1.json | 2 ++ .../test_inputs/Scientific/C862.NA19238.json | 2 ++ .../test_inputs/Scientific/D5327.NA12878.json | 2 ++ .../test_inputs/Scientific/D5327.NA12891.json | 2 ++ .../test_inputs/Scientific/D5327.NA12892.json | 2 ++ .../Scientific/RP-1535.NA17-308.json | 3 +- .../ExternalExomeReprocessing.changelog.md | 5 +++ ...ernalExomeReprocessing.plumbing.input.json | 7 +++- .../exome/ExternalExomeReprocessing.wdl | 6 ++-- .../test_inputs/Plumbing/RP-929.NA12878.json | 6 ++++ ...ternalWholeGenomeReprocessing.changelog.md | 5 +++ .../wgs/ExternalWholeGenomeReprocessing.wdl | 6 ++-- .../test_inputs/Plumbing/G96830.NA12878.json | 1 + .../wgs/WholeGenomeReprocessing.changelog.md | 5 +++ .../wgs/WholeGenomeReprocessing.wdl | 5 ++- .../test_inputs/Plumbing/G96830.NA12878.json | 1 + .../get_changed_pipeline_worklow_test_args.sh | 2 +- tasks/broad/AggregatedBamQC.wdl | 3 ++ tasks/broad/BamToCram.wdl | 3 ++ tasks/broad/Funcotator.wdl | 3 ++ tasks/broad/SplitLargeReadGroup.wdl | 3 ++ tasks/broad/UnmappedBamToAlignedBam.wdl | 3 ++ tasks/broad/VariantCalling.wdl | 3 ++ .../CramToUnmappedBams.wdl | 3 ++ .../pipelines/commandline/ConfigParser.scala | 10 ++++++ .../commandline/CromwellEnvironment.scala | 11 +++++++ .../config/AnnotationFiltrationConfig.scala | 8 +++-- .../tester/AnnotationFiltrationTester.scala | 2 +- .../tester/CromwellWorkflowTester.scala | 4 +-- verification/VerifyArrays.wdl | 3 ++ verification/VerifyGermlineSingleSample.wdl | 3 ++ verification/VerifyJointGenotyping.wdl | 3 ++ verification/VerifyMetrics.wdl | 3 ++ verification/VerifyMultiSampleArrays.wdl | 3 ++ verification/VerifyReblockGVCF.wdl | 3 ++ verification/VerifyReprocessing.wdl | 3 ++ verification/VerifySomaticSingleSample.wdl | 3 ++ verification/VerifyValidateChip.wdl | 33 ++++++++++--------- 71 files changed, 274 insertions(+), 40 deletions(-) diff --git a/pipelines/broad/annotation_filtration/AnnotationFiltration.changelog.md b/pipelines/broad/annotation_filtration/AnnotationFiltration.changelog.md index 8d22fb4256..5493540087 100644 --- 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 index e64e6008b8..62e3c281bb 100644 --- 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 index b26be2f8be..c7c29ec63b 100644 --- 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 index 33db309e64..c8a067df36 100644 --- 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 index eca1c8e6b0..679cfd0543 100644 --- 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 index cbf5e02f52..594a604ca2 100644 --- 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 index de7d9304a2..c57bd26bed 100644 --- 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 index 646c74234f..37fb2a2a7c 100644 --- 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 index e6f006935f..0a66750a6f 100644 --- 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 index 636b5226b0..3d58551f71 100644 --- 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/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md index 39598874d9..bd27eef19d 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md +++ b/pipelines/broad/dna_seq/germline/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/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl index dce40d2dd1..e14d8eb66a 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl +++ b/pipelines/broad/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/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md index ef501ade0b..a6c88fc3ab 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md +++ b/pipelines/broad/dna_seq/germline/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/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl index 307fd5123d..18fed56b46 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl +++ b/pipelines/broad/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/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md index 86cbf73c46..8750a67081 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md +++ b/pipelines/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. \ No newline at end of file diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl index 68b71f71f5..bf7f3c40ee 100644 --- 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/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md b/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md index 163447f8d5..43eeb34d96 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md +++ b/pipelines/broad/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 index 28c61b35ae..477f05677c 100644 --- 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/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Plumbing/RP-929.NA12878.json b/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Plumbing/RP-929.NA12878.json index a63205e512..caed387af3 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Plumbing/RP-929.NA12878.json +++ b/pipelines/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/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/C1963.CHMI_CHMI3_Nex1.json b/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/C1963.CHMI_CHMI3_Nex1.json index c7b9cc2241..b6e65f8f38 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/C1963.CHMI_CHMI3_Nex1.json +++ b/pipelines/broad/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/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/C862.NA19238.json b/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/C862.NA19238.json index 8737dc9dd5..6808280af8 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/C862.NA19238.json +++ b/pipelines/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/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12878.json b/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12878.json index e289f92d60..5731bd3ba2 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12878.json +++ b/pipelines/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/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12891.json b/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12891.json index cb78b5dfb8..7eca86e919 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12891.json +++ b/pipelines/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/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12892.json b/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12892.json index 9bd39c6084..4c7e604bc5 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/D5327.NA12892.json +++ b/pipelines/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/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/RP-1535.NA17-308.json b/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/RP-1535.NA17-308.json index 6c26f45d9f..c8ba0634a4 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/exome/test_inputs/Scientific/RP-1535.NA17-308.json +++ b/pipelines/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/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md b/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md index 61c889749c..df40acd535 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md +++ b/pipelines/broad/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 index de162d2c64..2888e7eec7 100644 --- 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 index 490a4df90e..ea56691e49 100644 --- 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 index 89bad7f15c..8394b22d8b 100644 --- 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 index 2e60c00b08..fa274b05be 100644 --- 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 index a68a276d7e..294a81c56d 100644 --- 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 index 7e84fe11be..2bc0881ca1 100644 --- 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 + } } diff --git a/pipelines/broad/reprocessing/exome/test_inputs/Plumbing/RP-929.NA12878.json b/pipelines/broad/reprocessing/exome/test_inputs/Plumbing/RP-929.NA12878.json index 53a3381d1c..1944727df4 100644 --- a/pipelines/broad/reprocessing/exome/test_inputs/Plumbing/RP-929.NA12878.json +++ b/pipelines/broad/reprocessing/exome/test_inputs/Plumbing/RP-929.NA12878.json @@ -53,6 +53,9 @@ "preemptible_tries": 3, "agg_preemptible_tries": 3 }, + "ExomeReprocessing.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false diff --git a/pipelines/broad/reprocessing/exome/test_inputs/Scientific/C1963.CHMI_CHMI3_Nex1.json b/pipelines/broad/reprocessing/exome/test_inputs/Scientific/C1963.CHMI_CHMI3_Nex1.json index ef40b058a7..3bc38756aa 100644 --- a/pipelines/broad/reprocessing/exome/test_inputs/Scientific/C1963.CHMI_CHMI3_Nex1.json +++ b/pipelines/broad/reprocessing/exome/test_inputs/Scientific/C1963.CHMI_CHMI3_Nex1.json @@ -53,6 +53,8 @@ "preemptible_tries": 3, "agg_preemptible_tries": 3 }, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false } diff --git a/pipelines/broad/reprocessing/exome/test_inputs/Scientific/C862.NA19238.json b/pipelines/broad/reprocessing/exome/test_inputs/Scientific/C862.NA19238.json index e5c4f8a675..11ed9cf775 100644 --- a/pipelines/broad/reprocessing/exome/test_inputs/Scientific/C862.NA19238.json +++ b/pipelines/broad/reprocessing/exome/test_inputs/Scientific/C862.NA19238.json @@ -52,6 +52,8 @@ "preemptible_tries": 3, "agg_preemptible_tries": 3 }, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false } \ No newline at end of file diff --git a/pipelines/broad/reprocessing/exome/test_inputs/Scientific/D5327.NA12878.json b/pipelines/broad/reprocessing/exome/test_inputs/Scientific/D5327.NA12878.json index b8c3b8ebe0..62fed91eab 100644 --- a/pipelines/broad/reprocessing/exome/test_inputs/Scientific/D5327.NA12878.json +++ b/pipelines/broad/reprocessing/exome/test_inputs/Scientific/D5327.NA12878.json @@ -54,6 +54,8 @@ "preemptible_tries": 3, "agg_preemptible_tries": 3 }, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false } diff --git a/pipelines/broad/reprocessing/exome/test_inputs/Scientific/D5327.NA12891.json b/pipelines/broad/reprocessing/exome/test_inputs/Scientific/D5327.NA12891.json index 299e3c8229..060bed656f 100644 --- a/pipelines/broad/reprocessing/exome/test_inputs/Scientific/D5327.NA12891.json +++ b/pipelines/broad/reprocessing/exome/test_inputs/Scientific/D5327.NA12891.json @@ -53,6 +53,8 @@ "preemptible_tries": 3, "agg_preemptible_tries": 3 }, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false } diff --git a/pipelines/broad/reprocessing/exome/test_inputs/Scientific/D5327.NA12892.json b/pipelines/broad/reprocessing/exome/test_inputs/Scientific/D5327.NA12892.json index 631ba276a0..bad45ab14f 100644 --- a/pipelines/broad/reprocessing/exome/test_inputs/Scientific/D5327.NA12892.json +++ b/pipelines/broad/reprocessing/exome/test_inputs/Scientific/D5327.NA12892.json @@ -56,6 +56,8 @@ "preemptible_tries": 3, "agg_preemptible_tries": 3 }, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false } diff --git a/pipelines/broad/reprocessing/exome/test_inputs/Scientific/RP-1535.NA17-308.json b/pipelines/broad/reprocessing/exome/test_inputs/Scientific/RP-1535.NA17-308.json index 9e9d29ac11..7defa7d3c7 100644 --- a/pipelines/broad/reprocessing/exome/test_inputs/Scientific/RP-1535.NA17-308.json +++ b/pipelines/broad/reprocessing/exome/test_inputs/Scientific/RP-1535.NA17-308.json @@ -53,7 +53,8 @@ "preemptible_tries": 3, "agg_preemptible_tries": 3 }, - + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, + "ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, "ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false } diff --git a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md index d0ff0ffe1e..385cca1ea8 100644 --- a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md +++ b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.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/external/exome/ExternalExomeReprocessing.plumbing.input.json b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.plumbing.input.json index 7a572e96e5..113700f9c2 100644 --- a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.plumbing.input.json +++ b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.plumbing.input.json @@ -53,6 +53,12 @@ "break_bands_at_multiples_of": 0 }, + "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.ApplyBQSR.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.10.1", + "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.BaseRecalibrator.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.10.1", + "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.GatherBqsrReports.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.10.1", + "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true, + "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, + "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false, "ExternalExomeReprocessing.ExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.ApplyBQSR.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.10.1", "ExternalExomeReprocessing.ExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.BaseRecalibrator.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.10.1", "ExternalExomeReprocessing.ExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.GatherBqsrReports.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.10.1", @@ -60,7 +66,6 @@ "ExternalExomeReprocessing.ExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, "ExternalExomeReprocessing.ExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false, - "ExternalExomeReprocessing.destination_cloud_path": "{DESTINATION_CLOUD_PATH}", "ExternalExomeReprocessing.vault_token_path": "{VAULT_TOKEN_PATH}", "ExternalExomeReprocessing.google_account_vault_path": "secret/dsde/gotc/prod/picard/picard-account.pem" diff --git a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl index 13c2fe8234..f002c804bd 100644 --- a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl +++ b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl @@ -5,7 +5,7 @@ import "../../../../../tasks/broad/CopyFilesFromCloudToCloud.wdl" as Copy workflow ExternalExomeReprocessing { - String pipeline_version = "2.0.2" + String pipeline_version = "2.1.0" input { File? input_cram @@ -157,5 +157,7 @@ workflow ExternalExomeReprocessing { File output_vcf = ExomeReprocessing.output_vcf File output_vcf_index = ExomeReprocessing.output_vcf_index } - + meta { + allowNestedInputs: true + } } diff --git a/pipelines/broad/reprocessing/external/exome/test_inputs/Plumbing/RP-929.NA12878.json b/pipelines/broad/reprocessing/external/exome/test_inputs/Plumbing/RP-929.NA12878.json index f5d13d1ef7..bd1a0717a4 100644 --- a/pipelines/broad/reprocessing/external/exome/test_inputs/Plumbing/RP-929.NA12878.json +++ b/pipelines/broad/reprocessing/external/exome/test_inputs/Plumbing/RP-929.NA12878.json @@ -53,6 +53,12 @@ "agg_preemptible_tries": 3 }, + "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.ApplyBQSR.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.10.1", + "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.BaseRecalibrator.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.10.1", + "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.GatherBqsrReports.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.10.1", + "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true, + "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics": false, + "ExternalExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics": false, "ExternalExomeReprocessing.ExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.ApplyBQSR.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.10.1", "ExternalExomeReprocessing.ExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.BaseRecalibrator.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.10.1", "ExternalExomeReprocessing.ExomeReprocessing.ExomeReprocessing.ExomeGermlineSingleSample.ExomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.GatherBqsrReports.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.10.1", diff --git a/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md b/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md index 2f02264046..68017ed8ba 100644 --- a/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md +++ b/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md @@ -1,3 +1,8 @@ +# 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 + # 1.0.2 2020-07-31 diff --git a/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl b/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl index e8da09a221..a923bd6093 100644 --- a/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl +++ b/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl @@ -5,7 +5,7 @@ import "../../../../../tasks/broad/CopyFilesFromCloudToCloud.wdl" as Copy workflow ExternalWholeGenomeReprocessing { - String pipeline_version = "1.0.2" + String pipeline_version = "1.1.0" input { File? input_cram @@ -167,5 +167,7 @@ workflow ExternalWholeGenomeReprocessing { File output_vcf = WholeGenomeReprocessing.output_vcf File output_vcf_index = WholeGenomeReprocessing.output_vcf_index } - + meta { + allowNestedInputs: true + } } diff --git a/pipelines/broad/reprocessing/external/wgs/test_inputs/Plumbing/G96830.NA12878.json b/pipelines/broad/reprocessing/external/wgs/test_inputs/Plumbing/G96830.NA12878.json index c7d0e686ef..e1fa0ae743 100644 --- a/pipelines/broad/reprocessing/external/wgs/test_inputs/Plumbing/G96830.NA12878.json +++ b/pipelines/broad/reprocessing/external/wgs/test_inputs/Plumbing/G96830.NA12878.json @@ -47,6 +47,7 @@ "ExternalWholeGenomeReprocessing.wgs_coverage_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_coverage_regions.hg38.interval_list", "ExternalWholeGenomeReprocessing.WholeGenomeReprocessing.WholeGenomeReprocessing.WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true, + "ExternalWholeGenomeReprocessing.WholeGenomeReprocessing.WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true, "ExternalWholeGenomeReprocessing.papi_settings": { "preemptible_tries": 3, diff --git a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md index 0b12b5e2ce..a0b5453561 100644 --- a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md +++ b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.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/wgs/WholeGenomeReprocessing.wdl b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.wdl index 6fa3eba634..997643402f 100644 --- a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.wdl +++ b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.wdl @@ -6,7 +6,7 @@ import "../../../../structs/dna_seq/DNASeqStructs.wdl" workflow WholeGenomeReprocessing { - String pipeline_version = "2.0.2" + String pipeline_version = "2.1.0" input { File? input_cram @@ -120,4 +120,7 @@ workflow WholeGenomeReprocessing { File output_vcf = WholeGenomeGermlineSingleSample.output_vcf File output_vcf_index = WholeGenomeGermlineSingleSample.output_vcf_index } + meta { + allowNestedInputs: true + } } diff --git a/pipelines/broad/reprocessing/wgs/test_inputs/Plumbing/G96830.NA12878.json b/pipelines/broad/reprocessing/wgs/test_inputs/Plumbing/G96830.NA12878.json index 1a81355534..8215e47a41 100644 --- a/pipelines/broad/reprocessing/wgs/test_inputs/Plumbing/G96830.NA12878.json +++ b/pipelines/broad/reprocessing/wgs/test_inputs/Plumbing/G96830.NA12878.json @@ -47,6 +47,7 @@ "WholeGenomeReprocessing.wgs_coverage_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_coverage_regions.hg38.interval_list", "WholeGenomeReprocessing.WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true, + "WholeGenomeReprocessing.WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check": true, "WholeGenomeReprocessing.papi_settings": { "preemptible_tries": 3, diff --git a/scripts/get_changed_pipeline_worklow_test_args.sh b/scripts/get_changed_pipeline_worklow_test_args.sh index 9fbd44d10a..77f405731d 100755 --- a/scripts/get_changed_pipeline_worklow_test_args.sh +++ b/scripts/get_changed_pipeline_worklow_test_args.sh @@ -17,7 +17,7 @@ function pipeline_to_args() { case ${pipeline} in AnnotationFiltration) - echo AnnotationFiltration -t ${test};; + echo AnnotationFiltration -t ${test} --env ${env};; Arrays) echo Arrays -a Single ${common_args};; MultiSampleArrays) diff --git a/tasks/broad/AggregatedBamQC.wdl b/tasks/broad/AggregatedBamQC.wdl index a6c8bed0f3..3a74aba746 100644 --- a/tasks/broad/AggregatedBamQC.wdl +++ b/tasks/broad/AggregatedBamQC.wdl @@ -106,4 +106,7 @@ input { File? fingerprint_summary_metrics = CheckFingerprint.summary_metrics File? fingerprint_detail_metrics = CheckFingerprint.detail_metrics } + meta { + allowNestedInputs: true + } } diff --git a/tasks/broad/BamToCram.wdl b/tasks/broad/BamToCram.wdl index 26f10d35b9..13b7272849 100644 --- a/tasks/broad/BamToCram.wdl +++ b/tasks/broad/BamToCram.wdl @@ -63,5 +63,8 @@ workflow BamToCram { File output_cram_md5 = ConvertToCram.output_cram_md5 File validate_cram_file_report = ValidateCram.report } + meta { + allowNestedInputs: true + } } diff --git a/tasks/broad/Funcotator.wdl b/tasks/broad/Funcotator.wdl index 1ed0248cad..dcb19c3b3d 100644 --- a/tasks/broad/Funcotator.wdl +++ b/tasks/broad/Funcotator.wdl @@ -77,6 +77,9 @@ workflow Funcotator { File funcotated_vcf_out = Funcotate.funcotated_vcf File funcotated_vcf_out_idx = Funcotate.funcotated_vcf_index } + meta { + allowNestedInputs: true + } } diff --git a/tasks/broad/SplitLargeReadGroup.wdl b/tasks/broad/SplitLargeReadGroup.wdl index 079e77f5db..6c4e13d82f 100644 --- a/tasks/broad/SplitLargeReadGroup.wdl +++ b/tasks/broad/SplitLargeReadGroup.wdl @@ -82,4 +82,7 @@ workflow SplitLargeReadGroup { output { File aligned_bam = GatherMonolithicBamFile.output_bam } + meta { + allowNestedInputs: true + } } diff --git a/tasks/broad/UnmappedBamToAlignedBam.wdl b/tasks/broad/UnmappedBamToAlignedBam.wdl index 3a3cf63647..29e77661eb 100644 --- a/tasks/broad/UnmappedBamToAlignedBam.wdl +++ b/tasks/broad/UnmappedBamToAlignedBam.wdl @@ -271,4 +271,7 @@ workflow UnmappedBamToAlignedBam { File output_bam = GatherBamFiles.output_bam File output_bam_index = GatherBamFiles.output_bam_index } + meta { + allowNestedInputs: true + } } diff --git a/tasks/broad/VariantCalling.wdl b/tasks/broad/VariantCalling.wdl index 7499243b51..63367c330a 100644 --- a/tasks/broad/VariantCalling.wdl +++ b/tasks/broad/VariantCalling.wdl @@ -153,6 +153,9 @@ workflow VariantCalling { File? bamout = MergeBamouts.output_bam File? bamout_index = MergeBamouts.output_bam_index } + meta { + allowNestedInputs: true + } } # This task is here because merging bamout files using Picard produces an error. diff --git a/tasks/broad/cram_to_unmapped_bams/CramToUnmappedBams.wdl b/tasks/broad/cram_to_unmapped_bams/CramToUnmappedBams.wdl index 3318d83254..e252ef5c05 100644 --- a/tasks/broad/cram_to_unmapped_bams/CramToUnmappedBams.wdl +++ b/tasks/broad/cram_to_unmapped_bams/CramToUnmappedBams.wdl @@ -88,6 +88,9 @@ workflow CramToUnmappedBams { Array[File] validation_report = ValidateSamFile.report Array[File] unmapped_bams = SortSam.output_bam } + meta { + allowNestedInputs: true + } } task RevertSam { diff --git a/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/commandline/ConfigParser.scala b/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/commandline/ConfigParser.scala index 406ede32b8..ac572fec6f 100644 --- a/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/commandline/ConfigParser.scala +++ b/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/commandline/ConfigParser.scala @@ -175,6 +175,16 @@ class ConfigParser annotationFiltrationConfig = config.annotationFiltrationConfig.copy(category = test) ) + }, + opt[CromwellEnvironment]('e', "env") + .text( + s"The environment that this should run in ${CromwellEnvironment.optionsString}" + ) + .required() + .action { (env, config) => + config.copy( + annotationFiltrationConfig = config.annotationFiltrationConfig.copy(env = env) + ) } ) diff --git a/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/commandline/CromwellEnvironment.scala b/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/commandline/CromwellEnvironment.scala index f0840d790a..f75f2f697d 100644 --- a/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/commandline/CromwellEnvironment.scala +++ b/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/commandline/CromwellEnvironment.scala @@ -38,6 +38,17 @@ object CromwellEnvironment extends Enum[CromwellEnvironment] { override val picardEnv: String = "prod" } + case object Test extends CromwellEnvironment { + override val cromwellUrl = new URL( + "https://cromwell-test.gotc-dev.broadinstitute.org" + ) + override val picardEnv: String = "dev" + override val environmentOptions: Seq[(String, Json)] = Seq( + "jes_gcs_root" -> "gs://broad-gotc-dev-execution1".asJson, + "google_project" -> "broad-exomes-dev1".asJson, + ) + } + case object Pharma5 extends CromwellEnvironment { override val cromwellUrl = new URL( "https://cromwell-pharma5.gotc-prod.broadinstitute.org" diff --git a/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/config/AnnotationFiltrationConfig.scala b/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/config/AnnotationFiltrationConfig.scala index 0f45c06c7b..dfba7889ae 100644 --- a/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/config/AnnotationFiltrationConfig.scala +++ b/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/config/AnnotationFiltrationConfig.scala @@ -1,7 +1,11 @@ package org.broadinstitute.dsp.pipelines.config -import org.broadinstitute.dsp.pipelines.commandline.WorkflowTestCategory +import org.broadinstitute.dsp.pipelines.commandline.{ + CromwellEnvironment, + WorkflowTestCategory +} case class AnnotationFiltrationConfig( - category: WorkflowTestCategory = WorkflowTestCategory.Plumbing + category: WorkflowTestCategory = WorkflowTestCategory.Plumbing, + env: CromwellEnvironment = CromwellEnvironment.Dev ) diff --git a/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/tester/AnnotationFiltrationTester.scala b/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/tester/AnnotationFiltrationTester.scala index e34c30ba91..218d4167a7 100644 --- a/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/tester/AnnotationFiltrationTester.scala +++ b/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/tester/AnnotationFiltrationTester.scala @@ -23,7 +23,7 @@ class AnnotationFiltrationTester(testConfig: AnnotationFiltrationConfig)( as: ActorSystem ) extends CromwellWorkflowTester { - override val env = CromwellEnvironment.Dev + override val env: CromwellEnvironment = testConfig.env override val workflowName = "AnnotationFiltration" diff --git a/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/tester/CromwellWorkflowTester.scala b/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/tester/CromwellWorkflowTester.scala index f3a7af757b..61d9f42d95 100644 --- a/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/tester/CromwellWorkflowTester.scala +++ b/tests/broad/scala_test/src/main/scala/org/broadinstitute/dsp/pipelines/tester/CromwellWorkflowTester.scala @@ -105,7 +105,7 @@ object CromwellWorkflowTester { wdlPath.pathAsString, tmp.pathAsString, DsdePipelinesGitHash, - env.entryName.toLowerCase + env.picardEnv ) ).!! tmp @@ -128,7 +128,7 @@ abstract class CromwellWorkflowTester( protected def env: CromwellEnvironment - protected lazy val envString: String = env.entryName.toLowerCase + protected lazy val envString: String = env.picardEnv def workflowName: String diff --git a/verification/VerifyArrays.wdl b/verification/VerifyArrays.wdl index f88553e55a..08d8babe47 100644 --- a/verification/VerifyArrays.wdl +++ b/verification/VerifyArrays.wdl @@ -94,6 +94,9 @@ workflow VerifyArrays { file1 = test_red_idat_md5, file2 = truth_red_idat_md5 } + meta { + allowNestedInputs: true + } } task CompareGtcs { diff --git a/verification/VerifyGermlineSingleSample.wdl b/verification/VerifyGermlineSingleSample.wdl index dca86dad4d..efeb938239 100755 --- a/verification/VerifyGermlineSingleSample.wdl +++ b/verification/VerifyGermlineSingleSample.wdl @@ -47,6 +47,9 @@ workflow VerifyGermlineSingleSample { output { Array[File] metric_comparison_report_files = CompareMetrics.metric_comparison_report_files } + meta { + allowNestedInputs: true + } } task CompareGvcfs { diff --git a/verification/VerifyJointGenotyping.wdl b/verification/VerifyJointGenotyping.wdl index 65c7d57411..d17752b96c 100644 --- a/verification/VerifyJointGenotyping.wdl +++ b/verification/VerifyJointGenotyping.wdl @@ -45,6 +45,9 @@ workflow VerifyJointGenotyping { test_fingerprint = test_fingerprint, truth_fingerprint = truth_fingerprint } + meta { + allowNestedInputs: true + } } task CompareFingerprints { diff --git a/verification/VerifyMetrics.wdl b/verification/VerifyMetrics.wdl index 931f637b31..abce1e29b4 100644 --- a/verification/VerifyMetrics.wdl +++ b/verification/VerifyMetrics.wdl @@ -28,6 +28,9 @@ workflow VerifyMetrics { output { Array[File] metric_comparison_report_files = CompareMetricFiles.report_file } + meta { + allowNestedInputs: true + } } task CompareTwoNumbers { diff --git a/verification/VerifyMultiSampleArrays.wdl b/verification/VerifyMultiSampleArrays.wdl index 53d21090b3..e6970c2ebb 100644 --- a/verification/VerifyMultiSampleArrays.wdl +++ b/verification/VerifyMultiSampleArrays.wdl @@ -29,4 +29,7 @@ workflow VerifyMultiSampleArrays { file1 = truth_vcf, file2 = test_vcf } + meta { + allowNestedInputs: true + } } diff --git a/verification/VerifyReblockGVCF.wdl b/verification/VerifyReblockGVCF.wdl index 5e2e8d9297..3d9d66aa40 100644 --- a/verification/VerifyReblockGVCF.wdl +++ b/verification/VerifyReblockGVCF.wdl @@ -14,4 +14,7 @@ workflow VerifyReblockGVCF { file1 = test_gvcf, file2 = truth_gvcf } + meta { + allowNestedInputs: true + } } \ No newline at end of file diff --git a/verification/VerifyReprocessing.wdl b/verification/VerifyReprocessing.wdl index 25f3413df2..074b7a483f 100644 --- a/verification/VerifyReprocessing.wdl +++ b/verification/VerifyReprocessing.wdl @@ -38,6 +38,9 @@ workflow VerifyReprocessing { truth_gvcf = truth_gvcf, test_gvcf = test_gvcf } + meta { + allowNestedInputs: true + } } struct BamPair { diff --git a/verification/VerifySomaticSingleSample.wdl b/verification/VerifySomaticSingleSample.wdl index f4e7ba1c9d..0f8c269e30 100755 --- a/verification/VerifySomaticSingleSample.wdl +++ b/verification/VerifySomaticSingleSample.wdl @@ -38,5 +38,8 @@ workflow VerifySomaticSingleSample { output { Array[File] metric_comparison_report_files = CompareMetrics.metric_comparison_report_files } + meta { + allowNestedInputes: true + } } diff --git a/verification/VerifyValidateChip.wdl b/verification/VerifyValidateChip.wdl index 67d4dbd38d..9eafdfb86c 100644 --- a/verification/VerifyValidateChip.wdl +++ b/verification/VerifyValidateChip.wdl @@ -44,21 +44,24 @@ workflow VerifyValidateChip { bead_pool_manifest_file=bead_pool_manifest_file } - call Tasks.CompareVcfs as CompareOutputVcfs { - input: - file1=truth_vcf, - file2=test_vcf - } + call Tasks.CompareVcfs as CompareOutputVcfs { + input: + file1=truth_vcf, + file2=test_vcf + } - call Tasks.CompareVcfs as CompareGenotypeConcordanceVcfs { - input: - file1=truth_genotype_concordance_vcf, - file2=test_genotype_concordance_vcf - } + call Tasks.CompareVcfs as CompareGenotypeConcordanceVcfs { + input: + file1=truth_genotype_concordance_vcf, + file2=test_genotype_concordance_vcf + } - call Tasks.CompareVcfs as CompareIndelGenotypeConcordanceVcfs { - input: - file1=truth_indel_genotype_concordance_vcf, - file2=test_indel_genotype_concordance_vcf - } + call Tasks.CompareVcfs as CompareIndelGenotypeConcordanceVcfs { + input: + file1=truth_indel_genotype_concordance_vcf, + file2=test_indel_genotype_concordance_vcf + } + meta { + allowNestedInputs: true + } } \ No newline at end of file