From 8e2828b9a9cca44925e1be80688e857fcb9f2824 Mon Sep 17 00:00:00 2001 From: Vahid Date: Fri, 2 Feb 2024 06:53:19 -0800 Subject: [PATCH] Replace sv_pipeline_base_docker with sv_pipeline_docker (#634) --- .../CleanVcf.SingleBatch.json.tmpl | 1 - .../CleanVcf.json.tmpl | 1 - .../ClusterBatch.json.tmpl | 1 - .../GatherSampleEvidence.json.tmpl | 1 - .../GenerateBatchMetrics.json.tmpl | 1 - .../GenotypeBatch.SingleBatch.json.tmpl | 1 - .../GenotypeBatch.json.tmpl | 1 - .../MakeCohortVcf.SingleBatch.json.tmpl | 1 - .../MakeCohortVcf.json.tmpl | 1 - .../RegenotypeCNVs.SingleBatch.json.tmpl | 1 - .../RegenotypeCNVs.json.tmpl | 1 - .../TrainGCNV.json.tmpl | 2 +- .../cohort_mode/workspace.tsv.tmpl | 1 - ...TKSVPipelineSingleSample.no_melt.json.tmpl | 1 - .../single_sample/workspace.tsv.tmpl | 1 - .../test/ClusterBatch/ClusterBatch.json.tmpl | 1 - .../test/FilterBatch/FilterBatch.json.tmpl | 1 - ...PipelineBatch.FromSampleEvidence.json.tmpl | 1 - .../GATKSVPipelineBatch.json.tmpl | 1 - .../GATKSVPipelinePhase1.json.tmpl | 1 - .../GATKSVPipelineSingleSample.json.tmpl | 1 - ...TKSVPipelineSingleSample.no_melt.json.tmpl | 1 - .../GatherSampleEvidence.json.tmpl | 1 - .../GatherSampleEvidenceBatch.json.tmpl | 1 - .../GenerateBatchMetrics.json.tmpl | 1 - .../GenotypeBatch/GenotypeBatch.json.tmpl | 1 - .../test/MakeCohortVcf/CleanVcf.json.tmpl | 1 - .../MakeCohortVcf/MakeCohortVcf.json.tmpl | 1 - .../RegenotypeCNVs/RegenotypeCNVs.json.tmpl | 1 - inputs/values/dockers.json | 1 - inputs/values/dockers_azure.json | 1 - wdl/CleanVcf.wdl | 3 +- wdl/ClusterBatch.wdl | 3 +- wdl/ClusterBatchMetrics.wdl | 12 ++-- wdl/CombineReassess.wdl | 7 +-- wdl/FilterBatch.wdl | 3 +- wdl/FilterBatchMetrics.wdl | 8 +-- wdl/GATKSVPipelineBatch.wdl | 12 +--- wdl/GATKSVPipelinePhase1.wdl | 7 +-- wdl/GATKSVPipelineSingleSample.wdl | 13 ++--- wdl/GATKSVPipelineSingleSampleMetrics.wdl | 18 +++--- wdl/GatherBatchEvidence.wdl | 3 +- wdl/GatherBatchEvidenceMetrics.wdl | 20 +++---- wdl/GatherSampleEvidence.wdl | 3 +- wdl/GatherSampleEvidenceBatch.wdl | 2 - wdl/GatherSampleEvidenceMetrics.wdl | 28 +++++----- wdl/GenerateBatchMetrics.wdl | 11 ++-- wdl/GenerateBatchMetricsMetrics.wdl | 6 +- wdl/GenotypeBatch.wdl | 3 +- wdl/GenotypeBatchMetrics.wdl | 14 ++--- wdl/MakeCohortVcf.wdl | 2 - wdl/MakeCohortVcfMetrics.wdl | 10 ++-- wdl/RegenotypeCNVs.wdl | 2 - wdl/SingleSampleFiltering.wdl | 4 +- wdl/TestUtils.wdl | 56 +++++++++---------- wdl/TrainGCNV.wdl | 8 +-- wdl/Utils.wdl | 12 ++-- 57 files changed, 122 insertions(+), 180 deletions(-) diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.SingleBatch.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.SingleBatch.json.tmpl index dc37d432f..87ffc1220 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.SingleBatch.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.SingleBatch.json.tmpl @@ -11,7 +11,6 @@ "CleanVcf.clean_vcf5_records_per_shard": 5000, "CleanVcf.primary_contigs_list": "${workspace.primary_contigs_list}", - "CleanVcf.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}", "CleanVcf.linux_docker": "${workspace.linux_docker}", "CleanVcf.sv_pipeline_docker": "${workspace.sv_pipeline_docker}", diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.json.tmpl index d2c5d265e..0c3abd33e 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.json.tmpl @@ -11,7 +11,6 @@ "CleanVcf.clean_vcf5_records_per_shard": 5000, "CleanVcf.primary_contigs_list": "${workspace.primary_contigs_list}", - "CleanVcf.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}", "CleanVcf.linux_docker": "${workspace.linux_docker}", "CleanVcf.sv_pipeline_docker": "${workspace.sv_pipeline_docker}", diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/ClusterBatch.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/ClusterBatch.json.tmpl index 714e889cd..4c9dcf45d 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/ClusterBatch.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/ClusterBatch.json.tmpl @@ -18,7 +18,6 @@ "ClusterBatch.sv_base_mini_docker": "${workspace.sv_base_mini_docker}", "ClusterBatch.sv_pipeline_docker": "${workspace.sv_pipeline_docker}", "ClusterBatch.gatk_docker": "${workspace.gatk_docker}", - "ClusterBatch.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}", "ClusterBatch.linux_docker": "${workspace.linux_docker}", "ClusterBatch.batch": "${this.sample_set_id}", diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GatherSampleEvidence.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GatherSampleEvidence.json.tmpl index b3af41cbc..2dd90c62a 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GatherSampleEvidence.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GatherSampleEvidence.json.tmpl @@ -27,7 +27,6 @@ "GatherSampleEvidence.cloud_sdk_docker": "${workspace.cloud_sdk_docker}", "GatherSampleEvidence.primary_contigs_fai": "${workspace.primary_contigs_fai}", - "GatherSampleEvidence.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}", "GatherSampleEvidence.bam_or_cram_file": "${this.bam_or_cram_file}", "GatherSampleEvidence.sample_id": "${this.sample_id}" diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenerateBatchMetrics.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenerateBatchMetrics.json.tmpl index 5ba5ee2fe..fc1e592bd 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenerateBatchMetrics.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenerateBatchMetrics.json.tmpl @@ -3,7 +3,6 @@ "GenerateBatchMetrics.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}", "GenerateBatchMetrics.sv_base_mini_docker": "${workspace.sv_base_mini_docker}", "GenerateBatchMetrics.sv_base_docker": "${workspace.sv_base_docker}", - "GenerateBatchMetrics.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}", "GenerateBatchMetrics.linux_docker" : "${workspace.linux_docker}", "GenerateBatchMetrics.BAF_split_size": "10000", diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.SingleBatch.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.SingleBatch.json.tmpl index f7a2ec295..f86aea972 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.SingleBatch.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.SingleBatch.json.tmpl @@ -12,7 +12,6 @@ "GenotypeBatch.ref_dict": "${workspace.reference_dict}", "GenotypeBatch.primary_contigs_list": "${workspace.primary_contigs_list}", - "GenotypeBatch.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}", "GenotypeBatch.batch": "${this.sample_set_id}", "GenotypeBatch.rf_cutoffs": "${this.cutoffs}", diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.json.tmpl index 172a8e3b0..a5bf747f9 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.json.tmpl @@ -12,7 +12,6 @@ "GenotypeBatch.ref_dict": "${workspace.reference_dict}", "GenotypeBatch.primary_contigs_list": "${workspace.primary_contigs_list}", - "GenotypeBatch.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}", "GenotypeBatch.batch": "${this.sample_set_id}", "GenotypeBatch.rf_cutoffs": "${this.cutoffs}", diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.SingleBatch.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.SingleBatch.json.tmpl index 5e6b2084b..c08470363 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.SingleBatch.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.SingleBatch.json.tmpl @@ -34,7 +34,6 @@ "MakeCohortVcf.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}", "MakeCohortVcf.primary_contigs_list": "${workspace.primary_contigs_list}", - "MakeCohortVcf.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}", "MakeCohortVcf.chr_x": "${workspace.chr_x}", "MakeCohortVcf.chr_y": "${workspace.chr_y}", diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.json.tmpl index b70f15fc8..759c6c2d8 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.json.tmpl @@ -34,7 +34,6 @@ "MakeCohortVcf.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}", "MakeCohortVcf.primary_contigs_list": "${workspace.primary_contigs_list}", - "MakeCohortVcf.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}", "MakeCohortVcf.chr_x": "${workspace.chr_x}", "MakeCohortVcf.chr_y": "${workspace.chr_y}", diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.SingleBatch.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.SingleBatch.json.tmpl index 72b8a7898..ba6971e90 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.SingleBatch.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.SingleBatch.json.tmpl @@ -1,6 +1,5 @@ { "RegenotypeCNVs.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}", - "RegenotypeCNVs.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}", "RegenotypeCNVs.sv_base_mini_docker": "${workspace.sv_base_mini_docker}", "RegenotypeCNVs.sv_pipeline_docker": "${workspace.sv_pipeline_docker}", "RegenotypeCNVs.n_RdTest_bins": "100000", diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.json.tmpl index 98ab1811c..2d4ec343f 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.json.tmpl @@ -1,6 +1,5 @@ { "RegenotypeCNVs.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}", - "RegenotypeCNVs.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}", "RegenotypeCNVs.sv_base_mini_docker": "${workspace.sv_base_mini_docker}", "RegenotypeCNVs.sv_pipeline_docker": "${workspace.sv_pipeline_docker}", "RegenotypeCNVs.n_RdTest_bins": "100000", diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/TrainGCNV.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/TrainGCNV.json.tmpl index cdad18c67..d99462381 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/TrainGCNV.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/TrainGCNV.json.tmpl @@ -62,5 +62,5 @@ "TrainGCNV.samples": "${this.samples.sample_id}", "TrainGCNV.n_samples_subsample": 100, - "TrainGCNV.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}" + "TrainGCNV.sv_pipeline_docker": "${workspace.sv_pipeline_docker}" } diff --git a/inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl index 39e0d3bd4..892b57b2b 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl @@ -10,7 +10,6 @@ manta_docker {{ dockers.manta_docker }} samtools_cloud_docker {{ dockers.samtools_cloud_docker }} sv_base_docker {{ dockers.sv_base_docker }} sv_base_mini_docker {{ dockers.sv_base_mini_docker }} -sv_pipeline_base_docker {{ dockers.sv_pipeline_base_docker }} sv_pipeline_docker {{ dockers.sv_pipeline_docker }} sv_pipeline_hail_docker {{ dockers.sv_pipeline_hail_docker }} sv_pipeline_updates_docker {{ dockers.sv_pipeline_updates_docker }} diff --git a/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl b/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl index 565512d85..825909481 100644 --- a/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl +++ b/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl @@ -33,7 +33,6 @@ "GATKSVPipelineSingleSample.linux_docker" : "${workspace.linux_docker}", "GATKSVPipelineSingleSample.manta_docker": "${workspace.manta_docker}", "GATKSVPipelineSingleSample.sv_base_docker": "${workspace.sv_base_docker}", - "GATKSVPipelineSingleSample.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}", "GATKSVPipelineSingleSample.sv_base_mini_docker": "${workspace.sv_base_mini_docker}", "GATKSVPipelineSingleSample.sv_pipeline_docker": "${workspace.sv_pipeline_docker}", "GATKSVPipelineSingleSample.sv_pipeline_hail_docker": "${workspace.sv_pipeline_hail_docker}", diff --git a/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl b/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl index 82709000a..05cae6c2d 100644 --- a/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl +++ b/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl @@ -9,7 +9,6 @@ manta_docker {{ dockers.manta_docker }} samtools_cloud_docker {{ dockers.samtools_cloud_docker }} sv_base_docker {{ dockers.sv_base_docker }} sv_base_mini_docker {{ dockers.sv_base_mini_docker }} -sv_pipeline_base_docker {{ dockers.sv_pipeline_base_docker }} sv_pipeline_docker {{ dockers.sv_pipeline_docker }} sv_pipeline_hail_docker {{ dockers.sv_pipeline_hail_docker }} sv_pipeline_updates_docker {{ dockers.sv_pipeline_updates_docker }} diff --git a/inputs/templates/test/ClusterBatch/ClusterBatch.json.tmpl b/inputs/templates/test/ClusterBatch/ClusterBatch.json.tmpl index 00225f1f7..29657d30a 100644 --- a/inputs/templates/test/ClusterBatch/ClusterBatch.json.tmpl +++ b/inputs/templates/test/ClusterBatch/ClusterBatch.json.tmpl @@ -20,7 +20,6 @@ "ClusterBatch.depth_clustering_algorithm": "SINGLE_LINKAGE", "ClusterBatch.gatk_docker": {{ dockers.gatk_docker | tojson }}, - "ClusterBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "ClusterBatch.linux_docker": {{ dockers.linux_docker | tojson }}, "ClusterBatch.batch": {{ test_batch.name | tojson }}, diff --git a/inputs/templates/test/FilterBatch/FilterBatch.json.tmpl b/inputs/templates/test/FilterBatch/FilterBatch.json.tmpl index dacb20f85..64e97714b 100644 --- a/inputs/templates/test/FilterBatch/FilterBatch.json.tmpl +++ b/inputs/templates/test/FilterBatch/FilterBatch.json.tmpl @@ -6,7 +6,6 @@ "FilterBatch.outlier_cutoff_nIQR": "10000", "FilterBatch.primary_contigs_list": {{ reference_resources.primary_contigs_list | tojson }}, - "FilterBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "FilterBatch.ped_file": {{ test_batch.ped_file | tojson }}, "FilterBatch.batch": {{ test_batch.name | tojson }}, diff --git a/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl b/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl index 462cbfda3..748d07ab4 100644 --- a/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl +++ b/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl @@ -29,7 +29,6 @@ "GATKSVPipelineBatch.condense_counts_docker" : {{ dockers.condense_counts_docker | tojson }}, "GATKSVPipelineBatch.genomes_in_the_cloud_docker" : {{ dockers.genomes_in_the_cloud_docker | tojson }}, "GATKSVPipelineBatch.sv_base_docker": {{ dockers.sv_base_docker | tojson }}, - "GATKSVPipelineBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "GATKSVPipelineBatch.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }}, "GATKSVPipelineBatch.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}, "GATKSVPipelineBatch.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }}, diff --git a/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl b/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl index 4e925a3de..596ed3a8c 100644 --- a/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl +++ b/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl @@ -23,7 +23,6 @@ "GATKSVPipelineBatch.genomes_in_the_cloud_docker" : {{ dockers.genomes_in_the_cloud_docker | tojson }}, "GATKSVPipelineBatch.scramble_docker" : {{ dockers.scramble_docker | tojson }}, "GATKSVPipelineBatch.sv_base_docker": {{ dockers.sv_base_docker | tojson }}, - "GATKSVPipelineBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "GATKSVPipelineBatch.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }}, "GATKSVPipelineBatch.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}, "GATKSVPipelineBatch.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }}, diff --git a/inputs/templates/test/GATKSVPipelinePhase1/GATKSVPipelinePhase1.json.tmpl b/inputs/templates/test/GATKSVPipelinePhase1/GATKSVPipelinePhase1.json.tmpl index 471fe461a..ded1403e2 100644 --- a/inputs/templates/test/GATKSVPipelinePhase1/GATKSVPipelinePhase1.json.tmpl +++ b/inputs/templates/test/GATKSVPipelinePhase1/GATKSVPipelinePhase1.json.tmpl @@ -1,7 +1,6 @@ { "GATKSVPipelinePhase1.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }}, "GATKSVPipelinePhase1.sv_base_docker": {{ dockers.sv_base_docker | tojson }}, - "GATKSVPipelinePhase1.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "GATKSVPipelinePhase1.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}, "GATKSVPipelinePhase1.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }}, "GATKSVPipelinePhase1.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }}, diff --git a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl index c60129a43..9ab55a96b 100644 --- a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl +++ b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl @@ -31,7 +31,6 @@ "GATKSVPipelineSingleSample.melt_docker" : {{ dockers.melt_docker | tojson }}, "GATKSVPipelineSingleSample.scramble_docker" : {{ dockers.scramble_docker | tojson }}, "GATKSVPipelineSingleSample.sv_base_docker": {{ dockers.sv_base_docker | tojson }}, - "GATKSVPipelineSingleSample.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "GATKSVPipelineSingleSample.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }}, "GATKSVPipelineSingleSample.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}, "GATKSVPipelineSingleSample.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }}, diff --git a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl index a265b5444..1f46cbb71 100644 --- a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl +++ b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl @@ -34,7 +34,6 @@ "GATKSVPipelineSingleSample.melt_docker": {{ dockers.melt_docker | tojson }}, "GATKSVPipelineSingleSample.scramble_docker": {{ dockers.scramble_docker | tojson }}, "GATKSVPipelineSingleSample.sv_base_docker": {{ dockers.sv_base_docker | tojson }}, - "GATKSVPipelineSingleSample.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "GATKSVPipelineSingleSample.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }}, "GATKSVPipelineSingleSample.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}, "GATKSVPipelineSingleSample.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }}, diff --git a/inputs/templates/test/GatherSampleEvidence/GatherSampleEvidence.json.tmpl b/inputs/templates/test/GatherSampleEvidence/GatherSampleEvidence.json.tmpl index 99ea705ba..111ca2bc3 100644 --- a/inputs/templates/test/GatherSampleEvidence/GatherSampleEvidence.json.tmpl +++ b/inputs/templates/test/GatherSampleEvidence/GatherSampleEvidence.json.tmpl @@ -21,7 +21,6 @@ "GatherSampleEvidence.samtools_cloud_docker": {{ dockers.samtools_cloud_docker | tojson }}, "GatherSampleEvidence.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }}, "GatherSampleEvidence.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}, - "GatherSampleEvidence.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "GatherSampleEvidence.manta_docker": {{ dockers.manta_docker | tojson }}, "GatherSampleEvidence.melt_docker" : {{ dockers.melt_docker | tojson }}, "GatherSampleEvidence.scramble_docker" : {{ dockers.scramble_docker | tojson }}, diff --git a/inputs/templates/test/GatherSampleEvidenceBatch/GatherSampleEvidenceBatch.json.tmpl b/inputs/templates/test/GatherSampleEvidenceBatch/GatherSampleEvidenceBatch.json.tmpl index 0f53b5083..ae822d558 100644 --- a/inputs/templates/test/GatherSampleEvidenceBatch/GatherSampleEvidenceBatch.json.tmpl +++ b/inputs/templates/test/GatherSampleEvidenceBatch/GatherSampleEvidenceBatch.json.tmpl @@ -29,7 +29,6 @@ "GatherSampleEvidenceBatch.batch": {{ test_batch.name | tojson }}, "GatherSampleEvidenceBatch.primary_contigs_fai": {{ reference_resources.primary_contigs_fai | tojson }}, - "GatherSampleEvidenceBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "GatherSampleEvidenceBatch.linux_docker": {{ dockers.linux_docker | tojson }}, "GatherSampleEvidenceBatch.bam_or_cram_files": {{ test_batch.bam_or_cram_files | tojson }}, diff --git a/inputs/templates/test/GenerateBatchMetrics/GenerateBatchMetrics.json.tmpl b/inputs/templates/test/GenerateBatchMetrics/GenerateBatchMetrics.json.tmpl index 8ff1ef8fb..98cc41866 100644 --- a/inputs/templates/test/GenerateBatchMetrics/GenerateBatchMetrics.json.tmpl +++ b/inputs/templates/test/GenerateBatchMetrics/GenerateBatchMetrics.json.tmpl @@ -3,7 +3,6 @@ "GenerateBatchMetrics.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }}, "GenerateBatchMetrics.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }}, "GenerateBatchMetrics.sv_base_docker": {{ dockers.sv_base_docker | tojson }}, - "GenerateBatchMetrics.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "GenerateBatchMetrics.linux_docker" : {{ dockers.linux_docker | tojson }}, "GenerateBatchMetrics.BAF_split_size": "10000", diff --git a/inputs/templates/test/GenotypeBatch/GenotypeBatch.json.tmpl b/inputs/templates/test/GenotypeBatch/GenotypeBatch.json.tmpl index 386086ff0..e1b94b9aa 100644 --- a/inputs/templates/test/GenotypeBatch/GenotypeBatch.json.tmpl +++ b/inputs/templates/test/GenotypeBatch/GenotypeBatch.json.tmpl @@ -12,7 +12,6 @@ "GenotypeBatch.ref_dict": {{ reference_resources.reference_dict | tojson }}, "GenotypeBatch.primary_contigs_list": {{ reference_resources.primary_contigs_list | tojson }}, - "GenotypeBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "GenotypeBatch.batch": {{ test_batch.name | tojson }}, "GenotypeBatch.rf_cutoffs": {{ test_batch.cutoffs | tojson }}, diff --git a/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl b/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl index f79f52fc6..8f562f162 100644 --- a/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl +++ b/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl @@ -11,7 +11,6 @@ "CleanVcf.clean_vcf5_records_per_shard": 5000, "CleanVcf.primary_contigs_list": {{ reference_resources.primary_contigs_list | tojson }}, - "CleanVcf.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "CleanVcf.linux_docker": {{ dockers.linux_docker | tojson }}, "CleanVcf.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}, diff --git a/inputs/templates/test/MakeCohortVcf/MakeCohortVcf.json.tmpl b/inputs/templates/test/MakeCohortVcf/MakeCohortVcf.json.tmpl index 718f5fb33..fbc5d2704 100644 --- a/inputs/templates/test/MakeCohortVcf/MakeCohortVcf.json.tmpl +++ b/inputs/templates/test/MakeCohortVcf/MakeCohortVcf.json.tmpl @@ -29,7 +29,6 @@ "MakeCohortVcf.random_seed": 0, "MakeCohortVcf.primary_contigs_list": {{ reference_resources.primary_contigs_list | tojson }}, - "MakeCohortVcf.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "MakeCohortVcf.linux_docker": {{ dockers.linux_docker | tojson }}, "MakeCohortVcf.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}, diff --git a/inputs/templates/test/RegenotypeCNVs/RegenotypeCNVs.json.tmpl b/inputs/templates/test/RegenotypeCNVs/RegenotypeCNVs.json.tmpl index 25415598e..970e89828 100644 --- a/inputs/templates/test/RegenotypeCNVs/RegenotypeCNVs.json.tmpl +++ b/inputs/templates/test/RegenotypeCNVs/RegenotypeCNVs.json.tmpl @@ -1,6 +1,5 @@ { "RegenotypeCNVs.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }}, - "RegenotypeCNVs.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }}, "RegenotypeCNVs.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }}, "RegenotypeCNVs.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}, "RegenotypeCNVs.n_RdTest_bins": "100000", diff --git a/inputs/values/dockers.json b/inputs/values/dockers.json index 3fa7a1b5d..8a55f572e 100644 --- a/inputs/values/dockers.json +++ b/inputs/values/dockers.json @@ -12,7 +12,6 @@ "samtools_cloud_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud:2024-01-24-v0.28.4-beta-9debd6d7", "sv_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base:2024-01-24-v0.28.4-beta-9debd6d7", "sv_base_mini_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base-mini:2024-01-24-v0.28.4-beta-9debd6d7", - "sv_pipeline_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7", "sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7", "sv_pipeline_hail_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7", "sv_pipeline_updates_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7", diff --git a/inputs/values/dockers_azure.json b/inputs/values/dockers_azure.json index 8880824f8..a054e6331 100644 --- a/inputs/values/dockers_azure.json +++ b/inputs/values/dockers_azure.json @@ -12,7 +12,6 @@ "samtools_cloud_docker": "vahid.azurecr.io/gatk-sv/samtools-cloud:2024-01-24-v0.28.4-beta-9debd6d7", "sv_base_docker": "vahid.azurecr.io/gatk-sv/sv-base:2024-01-24-v0.28.4-beta-9debd6d7", "sv_base_mini_docker": "vahid.azurecr.io/gatk-sv/sv-base-mini:2024-01-24-v0.28.4-beta-9debd6d7", - "sv_pipeline_base_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7", "sv_pipeline_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7", "sv_pipeline_hail_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7", "sv_pipeline_updates_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7", diff --git a/wdl/CleanVcf.wdl b/wdl/CleanVcf.wdl index 0694bc9a6..89532c1c2 100644 --- a/wdl/CleanVcf.wdl +++ b/wdl/CleanVcf.wdl @@ -35,7 +35,6 @@ workflow CleanVcf { # Module metrics parameters # Run module metrics workflow at the end - on by default Boolean? run_module_metrics - String? sv_pipeline_base_docker # required if run_module_metrics = true File? primary_contigs_list # required if run_module_metrics = true File? baseline_cluster_vcf # baseline files are optional for metrics workflow File? baseline_complex_resolve_vcf @@ -222,7 +221,7 @@ workflow CleanVcf { baseline_cleaned_vcf = baseline_cleaned_vcf, contig_list = select_first([primary_contigs_list]), linux_docker = linux_docker, - sv_pipeline_base_docker = select_first([sv_pipeline_base_docker]), + sv_pipeline_docker = sv_pipeline_docker, sv_base_mini_docker = sv_base_mini_docker } } diff --git a/wdl/ClusterBatch.wdl b/wdl/ClusterBatch.wdl index e6c55d5ae..f905f2943 100644 --- a/wdl/ClusterBatch.wdl +++ b/wdl/ClusterBatch.wdl @@ -56,7 +56,6 @@ workflow ClusterBatch { # Run module metrics workflow at the end - on by default Boolean? run_module_metrics String? linux_docker # required if run_module_metrics = true - String? sv_pipeline_base_docker # required if run_module_metrics = true File? baseline_depth_vcf # baseline files are optional for metrics workflow File? baseline_manta_vcf File? baseline_wham_vcf @@ -284,7 +283,7 @@ workflow ClusterBatch { baseline_melt_vcf = baseline_melt_vcf, contig_list = select_first([contig_list]), sv_base_mini_docker = sv_base_mini_docker, - sv_pipeline_base_docker = select_first([sv_pipeline_base_docker]), + sv_pipeline_docker = sv_pipeline_docker, linux_docker = select_first([linux_docker]) } } diff --git a/wdl/ClusterBatchMetrics.wdl b/wdl/ClusterBatchMetrics.wdl index b2bf397c5..8e55e540a 100644 --- a/wdl/ClusterBatchMetrics.wdl +++ b/wdl/ClusterBatchMetrics.wdl @@ -22,7 +22,7 @@ workflow ClusterBatchMetrics { File contig_list String? sv_base_mini_docker # required if not providing samples array - String sv_pipeline_base_docker + String sv_pipeline_docker String linux_docker RuntimeAttr? runtime_attr_sample_ids_from_vcf @@ -51,7 +51,7 @@ workflow ClusterBatchMetrics { prefix = "depth_clustered", types = "DEL,DUP", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_depth_metrics } if (defined(manta_vcf)) { @@ -63,7 +63,7 @@ workflow ClusterBatchMetrics { prefix = "manta_clustered", types = "DEL,DUP,INS,INV,BND", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_manta_metrics } } @@ -76,7 +76,7 @@ workflow ClusterBatchMetrics { prefix = "melt_clustered", types = "INS", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_melt_metrics } } @@ -89,7 +89,7 @@ workflow ClusterBatchMetrics { prefix = "scramble_clustered", types = "INS", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_scramble_metrics } } @@ -102,7 +102,7 @@ workflow ClusterBatchMetrics { prefix = "wham_clustered", types = "DEL,DUP", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_wham_metrics } } diff --git a/wdl/CombineReassess.wdl b/wdl/CombineReassess.wdl index 3409ce776..cc39506c6 100644 --- a/wdl/CombineReassess.wdl +++ b/wdl/CombineReassess.wdl @@ -10,7 +10,6 @@ workflow CombineReassess { Array[File] vcfs Int min_var_per_sample_outlier_threshold Float regeno_sample_overlap - String sv_pipeline_base_docker String sv_pipeline_docker RuntimeAttr? runtime_attr_vcf2bed RuntimeAttr? runtime_attr_merge_list_creassess @@ -33,7 +32,7 @@ workflow CombineReassess { min_var_per_sample_outlier_threshold = min_var_per_sample_outlier_threshold, regeno_sample_overlap = regeno_sample_overlap, runtime_attr_override = runtime_attr_merge_list_creassess, - sv_pipeline_base_docker = sv_pipeline_base_docker + sv_pipeline_docker = sv_pipeline_docker } output { File regeno_variants = MergeList.regeno_var @@ -88,7 +87,7 @@ task MergeList { File regeno_sample_ids_lookup Int min_var_per_sample_outlier_threshold Float regeno_sample_overlap - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } RuntimeAttr default_attr = object { @@ -175,7 +174,7 @@ task MergeList { memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB" disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD" bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker 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/wdl/FilterBatch.wdl b/wdl/FilterBatch.wdl index 15425844a..2705f5ea6 100644 --- a/wdl/FilterBatch.wdl +++ b/wdl/FilterBatch.wdl @@ -23,7 +23,6 @@ workflow FilterBatch { # Module metrics parameters # Run module metrics workflow at the end - on by default Boolean? run_module_metrics - String? sv_pipeline_base_docker # required if run_module_metrics = true File? primary_contigs_list # required if run_module_metrics = true File? ped_file # required if run_module_metrics = true File? baseline_filtered_depth_vcf # baseline files are optional for metrics workflow @@ -120,7 +119,7 @@ workflow FilterBatch { baseline_filtered_depth_vcf = baseline_filtered_depth_vcf, contig_list = select_first([primary_contigs_list]), linux_docker = linux_docker, - sv_pipeline_base_docker = select_first([sv_pipeline_base_docker]), + sv_pipeline_docker = sv_pipeline_docker, sv_base_mini_docker = sv_base_mini_docker } } diff --git a/wdl/FilterBatchMetrics.wdl b/wdl/FilterBatchMetrics.wdl index 97f9a7cdb..99fde42a9 100644 --- a/wdl/FilterBatchMetrics.wdl +++ b/wdl/FilterBatchMetrics.wdl @@ -21,7 +21,7 @@ workflow FilterBatchMetrics { File contig_list String linux_docker - String sv_pipeline_base_docker + String sv_pipeline_docker String sv_base_mini_docker RuntimeAttr? runtime_attr_subset_ped @@ -41,7 +41,7 @@ workflow FilterBatchMetrics { prefix = "filtered_pesr", types = "DEL,DUP,INS,INV,BND", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_pesr_vcf_metrics } @@ -53,7 +53,7 @@ workflow FilterBatchMetrics { prefix = "filtered_depth", types = "DEL,DUP", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_depth_vcf_metrics } @@ -72,7 +72,7 @@ workflow FilterBatchMetrics { outlier_list = outlier_list, filtered_ped_file = SubsetPedFile.ped_subset_file, samples = samples, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_cutoff_outlier_metrics } diff --git a/wdl/GATKSVPipelineBatch.wdl b/wdl/GATKSVPipelineBatch.wdl index 077b13100..0f81f8ffd 100644 --- a/wdl/GATKSVPipelineBatch.wdl +++ b/wdl/GATKSVPipelineBatch.wdl @@ -92,7 +92,6 @@ workflow GATKSVPipelineBatch { String sv_pipeline_hail_docker String sv_pipeline_updates_docker String sv_pipeline_rdtest_docker - String sv_pipeline_base_docker String sv_pipeline_qc_docker String linux_docker String cnmops_docker @@ -142,7 +141,6 @@ workflow GATKSVPipelineBatch { run_module_metrics = run_sampleevidence_metrics, primary_contigs_fai = primary_contigs_fai, batch = name, - sv_pipeline_base_docker = sv_pipeline_base_docker, linux_docker = linux_docker, sv_pipeline_docker=sv_pipeline_docker, sv_base_mini_docker=sv_base_mini_docker, @@ -227,7 +225,6 @@ workflow GATKSVPipelineBatch { primary_contigs_list = primary_contigs_list, sv_base_mini_docker=sv_base_mini_docker, sv_base_docker=sv_base_docker, - sv_pipeline_base_docker=sv_pipeline_base_docker, sv_pipeline_docker=sv_pipeline_docker, sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker, sv_pipeline_qc_docker=sv_pipeline_qc_docker, @@ -256,7 +253,6 @@ workflow GATKSVPipelineBatch { ref_dict=reference_dict, run_module_metrics = run_genotypebatch_metrics, primary_contigs_list = primary_contigs_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, sv_base_mini_docker=sv_base_mini_docker, sv_pipeline_docker=sv_pipeline_docker, sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker, @@ -278,8 +274,7 @@ workflow GATKSVPipelineBatch { regeno_coverage_medians=[GenotypeBatch.regeno_coverage_medians], sv_base_mini_docker=sv_base_mini_docker, sv_pipeline_docker=sv_pipeline_docker, - sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker, - sv_pipeline_base_docker=sv_pipeline_base_docker + sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker } @@ -307,7 +302,6 @@ workflow GATKSVPipelineBatch { median_coverage_files=[GATKSVPipelinePhase1.median_cov], run_module_metrics = run_makecohortvcf_metrics, primary_contigs_list = primary_contigs_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, linux_docker=linux_docker, sv_pipeline_docker=sv_pipeline_docker, sv_pipeline_hail_docker=sv_pipeline_hail_docker, @@ -340,7 +334,7 @@ workflow GATKSVPipelineBatch { samples = samples, test_metrics = CatBatchMetrics.out, base_metrics = CatBaselineMetrics.out, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_plot_metrics } } @@ -350,7 +344,7 @@ workflow GATKSVPipelineBatch { name = name, metrics = CatBatchMetrics.out, qc_definitions = qc_definitions, - sv_pipeline_base_docker = sv_pipeline_base_docker + sv_pipeline_docker = sv_pipeline_docker } scatter (i in range(length(samples))) { diff --git a/wdl/GATKSVPipelinePhase1.wdl b/wdl/GATKSVPipelinePhase1.wdl index 3aa03f739..e65b9926c 100644 --- a/wdl/GATKSVPipelinePhase1.wdl +++ b/wdl/GATKSVPipelinePhase1.wdl @@ -26,7 +26,6 @@ workflow GATKSVPipelinePhase1 { String sv_base_mini_docker String sv_base_docker - String sv_pipeline_base_docker String sv_pipeline_docker String sv_pipeline_rdtest_docker String sv_pipeline_qc_docker @@ -333,8 +332,7 @@ workflow GATKSVPipelinePhase1 { runtime_attr_postprocess = runtime_attr_postprocess, runtime_attr_explode = runtime_attr_explode, run_module_metrics = run_batchevidence_metrics, - primary_contigs_list = primary_contigs_list, - sv_pipeline_base_docker = sv_pipeline_base_docker + primary_contigs_list = primary_contigs_list } call clusterbatch.ClusterBatch as ClusterBatch { @@ -366,7 +364,6 @@ workflow GATKSVPipelinePhase1 { N_IQR_cutoff_plotting = N_IQR_cutoff_plotting, run_module_metrics=run_clusterbatch_metrics, linux_docker=linux_docker, - sv_pipeline_base_docker=sv_pipeline_base_docker, baseline_depth_vcf=baseline_depth_vcf_cluster_batch, baseline_manta_vcf=baseline_manta_vcf_cluster_batch, baseline_wham_vcf=baseline_wham_vcf_cluster_batch, @@ -422,7 +419,6 @@ workflow GATKSVPipelinePhase1 { allosome_contigs=allosome_contigs, sv_base_mini_docker=sv_base_mini_docker, sv_base_docker=sv_base_docker, - sv_pipeline_base_docker=sv_pipeline_base_docker, sv_pipeline_docker=sv_pipeline_docker, sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker, linux_docker=linux_docker, @@ -465,7 +461,6 @@ workflow GATKSVPipelinePhase1 { runtime_attr_filter_samples=runtime_attr_filter_samples, run_module_metrics = run_filterbatch_metrics, primary_contigs_list = primary_contigs_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, ped_file = ped_file } diff --git a/wdl/GATKSVPipelineSingleSample.wdl b/wdl/GATKSVPipelineSingleSample.wdl index 2394f9930..7870908ad 100644 --- a/wdl/GATKSVPipelineSingleSample.wdl +++ b/wdl/GATKSVPipelineSingleSample.wdl @@ -69,7 +69,6 @@ workflow GATKSVPipelineSingleSample { String sv_pipeline_hail_docker String sv_pipeline_updates_docker String sv_pipeline_rdtest_docker - String sv_pipeline_base_docker String sv_pipeline_qc_docker String linux_docker String cnmops_docker @@ -891,7 +890,6 @@ workflow GATKSVPipelineSingleSample { pesr_clustering_algorithm=pesr_clustering_algorithm, run_module_metrics=run_clusterbatch_metrics, linux_docker=linux_docker, - sv_pipeline_base_docker=sv_pipeline_base_docker, baseline_depth_vcf=baseline_depth_vcf_cluster_batch, baseline_manta_vcf=baseline_manta_vcf_cluster_batch, baseline_wham_vcf=baseline_wham_vcf_cluster_batch, @@ -1158,7 +1156,6 @@ workflow GATKSVPipelineSingleSample { run_module_metrics = run_makecohortvcf_metrics, primary_contigs_list=primary_contigs_list, - sv_pipeline_base_docker=sv_pipeline_base_docker, linux_docker=linux_docker, sv_pipeline_docker=sv_pipeline_docker, @@ -1342,7 +1339,7 @@ workflow GATKSVPipelineSingleSample { sample_counts = case_counts_file_, contig_list = primary_contigs_list, linux_docker = linux_docker, - sv_pipeline_base_docker = sv_pipeline_base_docker + sv_pipeline_docker = sv_pipeline_docker } call utils.RunQC as SampleFilterQC { @@ -1350,14 +1347,14 @@ workflow GATKSVPipelineSingleSample { name=batch, metrics=SampleFilterMetrics.metrics_file, qc_definitions = qc_definitions, - sv_pipeline_base_docker=sv_pipeline_base_docker + sv_pipeline_docker=sv_pipeline_docker } call SingleSampleFiltering.SampleQC as FilterSample { input: vcf=FilterVcfWithReferencePanelCalls.out, sample_filtering_qc_file=SampleFilterQC.out, - sv_pipeline_base_docker=sv_pipeline_base_docker, + sv_pipeline_docker=sv_pipeline_docker, } call annotate.AnnotateVcf { @@ -1413,7 +1410,7 @@ workflow GATKSVPipelineSingleSample { non_genotyped_unique_depth_calls_vcf = GetUniqueNonGenotypedDepthCalls.out, contig_list = primary_contigs_list, linux_docker = linux_docker, - sv_pipeline_base_docker = sv_pipeline_base_docker + sv_pipeline_docker = sv_pipeline_docker } call utils.RunQC as SingleSampleQC { @@ -1421,7 +1418,7 @@ workflow GATKSVPipelineSingleSample { name = batch, metrics = SingleSampleMetrics.metrics_file, qc_definitions = qc_definitions, - sv_pipeline_base_docker = sv_pipeline_base_docker + sv_pipeline_docker = sv_pipeline_docker } output { diff --git a/wdl/GATKSVPipelineSingleSampleMetrics.wdl b/wdl/GATKSVPipelineSingleSampleMetrics.wdl index 969884c01..8078203ed 100644 --- a/wdl/GATKSVPipelineSingleSampleMetrics.wdl +++ b/wdl/GATKSVPipelineSingleSampleMetrics.wdl @@ -27,7 +27,7 @@ workflow SingleSampleMetrics { File contig_list String linux_docker - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_sr_metrics RuntimeAttr? runtime_attr_pe_metrics @@ -47,7 +47,7 @@ workflow SingleSampleMetrics { input: sr_file = select_first([sample_sr]), samples = [case_sample], - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_sr_metrics } } @@ -57,7 +57,7 @@ workflow SingleSampleMetrics { input: pe_file = select_first([sample_pe]), samples = [case_sample], - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_pe_metrics } } @@ -67,7 +67,7 @@ workflow SingleSampleMetrics { input: counts_file = select_first([sample_counts]), sample_id = case_sample, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_counts_metrics } } @@ -81,7 +81,7 @@ workflow SingleSampleMetrics { prefix = "cleaned", types = "DEL,DUP,INS,INV,CTX,CNV,CPX,BND", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_vcf_metrics } } @@ -95,7 +95,7 @@ workflow SingleSampleMetrics { prefix = "final", types = "DEL,DUP,INS,INV,CTX,CNV,CPX,BND", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_vcf_metrics } } @@ -109,7 +109,7 @@ workflow SingleSampleMetrics { prefix = "genotyped_pesr", types = "DEL,DUP,INS,INV,BND", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_pesr_metrics } } @@ -123,7 +123,7 @@ workflow SingleSampleMetrics { prefix = "genotyped_depth", types = "DEL,DUP", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_depth_metrics } } @@ -137,7 +137,7 @@ workflow SingleSampleMetrics { prefix = "non_genotyped_uniq_depth", types = "DEL,DUP", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_unique_depth_metrics } } diff --git a/wdl/GatherBatchEvidence.wdl b/wdl/GatherBatchEvidence.wdl index 5817bca68..f3f01a7e1 100644 --- a/wdl/GatherBatchEvidence.wdl +++ b/wdl/GatherBatchEvidence.wdl @@ -129,7 +129,6 @@ workflow GatherBatchEvidence { # Module metrics parameters # Run module metrics workflow at the end - off by default for GatherBatchEvidence because of runtime/expense Boolean? run_module_metrics - String? sv_pipeline_base_docker # required if run_module_metrics = true File? primary_contigs_list # required if run_module_metrics = true # baseline files are optional for metrics workflow @@ -460,7 +459,7 @@ workflow GatherBatchEvidence { baseline_merged_dups = baseline_merged_dups, baseline_median_cov = baseline_median_cov, contig_list = select_first([primary_contigs_list]), - sv_pipeline_base_docker = select_first([sv_pipeline_base_docker]), + sv_pipeline_docker = sv_pipeline_docker, linux_docker = linux_docker } } diff --git a/wdl/GatherBatchEvidenceMetrics.wdl b/wdl/GatherBatchEvidenceMetrics.wdl index e3d257628..6a10bcbcb 100644 --- a/wdl/GatherBatchEvidenceMetrics.wdl +++ b/wdl/GatherBatchEvidenceMetrics.wdl @@ -20,7 +20,7 @@ workflow GatherBatchEvidenceMetrics { File? baseline_median_cov File contig_list - String sv_pipeline_base_docker + String sv_pipeline_docker String linux_docker RuntimeAttr? runtime_attr_baf_metrics @@ -40,28 +40,28 @@ workflow GatherBatchEvidenceMetrics { input: baf_file = merged_BAF, samples = samples, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = select_first([runtime_attr_baf_metrics, {"mem_gb": 30, "disk_gb": 100}]) } call tu.SRMetrics { input: sr_file = merged_SR, samples = samples, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = select_first([runtime_attr_sr_metrics, {"mem_gb": 30, "disk_gb": 100, "preemptible_tries": 0}]) } call tu.PEMetrics { input: pe_file = merged_PE, samples = samples, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = select_first([runtime_attr_pe_metrics, {"mem_gb": 15, "disk_gb": 100, "preemptible_tries": 0}]) } call tu.BincovMetrics { input: bincov_matrix = merged_bincov, samples = samples, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_bincov_metrics } call tu.MedcovMetrics { @@ -69,7 +69,7 @@ workflow GatherBatchEvidenceMetrics { medcov_file = median_cov, samples = samples, baseline_medcov_file = baseline_median_cov, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_medcov_metrics } if (defined(baseline_merged_dels)) { @@ -79,7 +79,7 @@ workflow GatherBatchEvidenceMetrics { baseline_bed = select_first([baseline_merged_dels]), type = "DEL", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_merged_del } } @@ -89,7 +89,7 @@ workflow GatherBatchEvidenceMetrics { bed = merged_dels, type = "DEL", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_merged_del } } @@ -100,7 +100,7 @@ workflow GatherBatchEvidenceMetrics { baseline_bed = select_first([baseline_merged_dups]), type = "DUP", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_merged_dup } } @@ -110,7 +110,7 @@ workflow GatherBatchEvidenceMetrics { bed = merged_dups, type = "DUP", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_merged_dup } } diff --git a/wdl/GatherSampleEvidence.wdl b/wdl/GatherSampleEvidence.wdl index f144bef4a..f440503c9 100644 --- a/wdl/GatherSampleEvidence.wdl +++ b/wdl/GatherSampleEvidence.wdl @@ -83,7 +83,6 @@ workflow GatherSampleEvidence { # Run module metrics workflow at the end - on by default Boolean run_module_metrics = true File? primary_contigs_fai # required if run_module_metrics = true - String? sv_pipeline_base_docker # required if run_module_metrics = true File? baseline_manta_vcf # baseline files are optional for metrics workflow File? baseline_wham_vcf File? baseline_melt_vcf @@ -289,7 +288,7 @@ workflow GatherSampleEvidence { baseline_wham_vcf = baseline_wham_vcf, contig_list = primary_contigs_list, contig_index = select_first([primary_contigs_fai]), - sv_pipeline_base_docker = select_first([sv_pipeline_base_docker]) + sv_pipeline_docker = sv_pipeline_docker } } diff --git a/wdl/GatherSampleEvidenceBatch.wdl b/wdl/GatherSampleEvidenceBatch.wdl index 3c6fa9f04..e5e45b181 100644 --- a/wdl/GatherSampleEvidenceBatch.wdl +++ b/wdl/GatherSampleEvidenceBatch.wdl @@ -61,7 +61,6 @@ workflow GatherSampleEvidenceBatch { # Run module metrics workflow at the end - on by default Boolean? run_module_metrics String? batch # required if run_module_metrics = true - String? sv_pipeline_base_docker # required if run_module_metrics = true String? linux_docker # required if run_module_metrics = true File? baseline_manta_vcf # baseline files are optional for metrics workflow File? baseline_wham_vcf @@ -135,7 +134,6 @@ workflow GatherSampleEvidenceBatch { scramble_part2_threads=scramble_part2_threads, wham_include_list_bed_file = wham_include_list_bed_file, run_module_metrics = run_module_metrics_, - sv_pipeline_base_docker = sv_pipeline_base_docker, baseline_manta_vcf = baseline_manta_vcf, baseline_melt_vcf = baseline_melt_vcf, baseline_scramble_vcf = baseline_scramble_vcf, diff --git a/wdl/GatherSampleEvidenceMetrics.wdl b/wdl/GatherSampleEvidenceMetrics.wdl index aba4f6bc2..ac972a4b2 100644 --- a/wdl/GatherSampleEvidenceMetrics.wdl +++ b/wdl/GatherSampleEvidenceMetrics.wdl @@ -21,7 +21,7 @@ workflow GatherSampleEvidenceMetrics { File contig_list File contig_index Int min_size = 50 - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_manta_std RuntimeAttr? runtime_attr_manta_metrics @@ -43,7 +43,7 @@ workflow GatherSampleEvidenceMetrics { caller = "manta", contig_index = contig_index, min_size = min_size, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_manta_std } if (defined(baseline_manta_vcf)) { @@ -54,7 +54,7 @@ workflow GatherSampleEvidenceMetrics { caller = "manta", contig_index = contig_index, min_size = min_size, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_manta_std } } @@ -66,7 +66,7 @@ workflow GatherSampleEvidenceMetrics { prefix = "manta_" + sample, types = "DEL,DUP,INS,INV,BND", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_manta_metrics } } @@ -78,7 +78,7 @@ workflow GatherSampleEvidenceMetrics { caller = "melt", contig_index = contig_index, min_size = min_size, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_melt_std } if (defined(baseline_melt_vcf)) { @@ -89,7 +89,7 @@ workflow GatherSampleEvidenceMetrics { caller = "melt", contig_index = contig_index, min_size = min_size, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_melt_std } } @@ -101,7 +101,7 @@ workflow GatherSampleEvidenceMetrics { prefix = "melt_" + sample, types = "DEL,DUP,INS,INV,BND", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_melt_metrics } } @@ -114,7 +114,7 @@ workflow GatherSampleEvidenceMetrics { prefix = "scramble_" + sample, types = "INS", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_scramble_metrics } } @@ -126,7 +126,7 @@ workflow GatherSampleEvidenceMetrics { caller = "wham", contig_index = contig_index, min_size = min_size, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_wham_std } if (defined(baseline_wham_vcf)) { @@ -137,7 +137,7 @@ workflow GatherSampleEvidenceMetrics { caller = "wham", contig_index = contig_index, min_size = min_size, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_wham_std } } @@ -149,7 +149,7 @@ workflow GatherSampleEvidenceMetrics { prefix = "wham_" + sample, types = "DEL,DUP,INS,INV,BND", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_wham_metrics } } @@ -158,7 +158,7 @@ workflow GatherSampleEvidenceMetrics { input: sr_file = select_first([pesr_split]), samples = [sample], - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_sr_metrics } } @@ -167,7 +167,7 @@ workflow GatherSampleEvidenceMetrics { input: pe_file = select_first([pesr_disc]), samples = [sample], - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_pe_metrics } } @@ -176,7 +176,7 @@ workflow GatherSampleEvidenceMetrics { input: counts_file = select_first([coverage_counts]), sample_id = sample, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_counts_metrics } } diff --git a/wdl/GenerateBatchMetrics.wdl b/wdl/GenerateBatchMetrics.wdl index 53c228b29..872150394 100644 --- a/wdl/GenerateBatchMetrics.wdl +++ b/wdl/GenerateBatchMetrics.wdl @@ -47,7 +47,6 @@ workflow GenerateBatchMetrics { String sv_pipeline_rdtest_docker String sv_base_mini_docker String sv_base_docker - String sv_pipeline_base_docker String linux_docker RuntimeAttr? runtime_attr_ids_from_vcf @@ -255,7 +254,7 @@ workflow GenerateBatchMetrics { batch = batch, input_metrics = select_all(AggregateTests.metrics), common = false, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_aggregate_callers } @@ -264,7 +263,7 @@ workflow GenerateBatchMetrics { batch = batch, input_metrics = select_all(AggregateTestsCommon.metrics), common = true, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_aggregate_callers } @@ -277,7 +276,7 @@ workflow GenerateBatchMetrics { metrics_common = AggregateCallersCommon.metrics, contig_list = select_first([primary_contigs_list]), linux_docker = linux_docker, - sv_pipeline_base_docker = sv_pipeline_base_docker + sv_pipeline_docker = sv_pipeline_docker } } @@ -442,7 +441,7 @@ task AggregateCallers { String batch Array[File] input_metrics Boolean common - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -480,7 +479,7 @@ task AggregateCallers { memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB" disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD" bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker 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/wdl/GenerateBatchMetricsMetrics.wdl b/wdl/GenerateBatchMetricsMetrics.wdl index c12684cbf..a3999ecfa 100644 --- a/wdl/GenerateBatchMetricsMetrics.wdl +++ b/wdl/GenerateBatchMetricsMetrics.wdl @@ -8,7 +8,7 @@ workflow GenerateBatchMetricsMetrics { File metrics File metrics_common File contig_list - String sv_pipeline_base_docker + String sv_pipeline_docker String linux_docker RuntimeAttr? runtime_attr_metrics_file_metrics @@ -22,7 +22,7 @@ workflow GenerateBatchMetricsMetrics { contig_list = contig_list, common = false, prefix = "GenerateBatchMetrics.non_common." + name, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_metrics_file_metrics } @@ -32,7 +32,7 @@ workflow GenerateBatchMetricsMetrics { contig_list = contig_list, common = true, prefix = "GenerateBatchMetrics.common." + name, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_common_metrics_metrics } diff --git a/wdl/GenotypeBatch.wdl b/wdl/GenotypeBatch.wdl index facb1ccfe..bba5f2fd3 100644 --- a/wdl/GenotypeBatch.wdl +++ b/wdl/GenotypeBatch.wdl @@ -42,7 +42,6 @@ workflow GenotypeBatch { # Module metrics parameters # Run module metrics workflow at the end - on by default Boolean? run_module_metrics - String? sv_pipeline_base_docker # required if run_module_metrics = true File? primary_contigs_list # required if run_module_metrics = true File? baseline_genotyped_depth_vcf # baseline files are optional for metrics workflow File? baseline_genotyped_pesr_vcf @@ -283,7 +282,7 @@ workflow GenotypeBatch { baseline_genotyped_depth_vcf = baseline_genotyped_depth_vcf, contig_list = select_first([primary_contigs_list]), linux_docker = linux_docker, - sv_pipeline_base_docker = select_first([sv_pipeline_base_docker]) + sv_pipeline_docker = sv_pipeline_docker } } diff --git a/wdl/GenotypeBatchMetrics.wdl b/wdl/GenotypeBatchMetrics.wdl index 8007ac677..49f85cf87 100644 --- a/wdl/GenotypeBatchMetrics.wdl +++ b/wdl/GenotypeBatchMetrics.wdl @@ -21,7 +21,7 @@ workflow GenotypeBatchMetrics { File contig_list String linux_docker - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_pesr_metrics RuntimeAttr? runtime_attr_depth_metrics @@ -38,7 +38,7 @@ workflow GenotypeBatchMetrics { prefix = "genotyped_pesr", types = "DEL,DUP,INS,INV,BND", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_pesr_metrics } @@ -50,7 +50,7 @@ workflow GenotypeBatchMetrics { prefix = "genotyped_depth", types = "DEL,DUP", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_depth_metrics } @@ -58,7 +58,7 @@ workflow GenotypeBatchMetrics { input: cutoffs = cutoffs_pesr_pesr, name = "pesr_pesr", - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_cutoff_metrics } @@ -66,7 +66,7 @@ workflow GenotypeBatchMetrics { input: cutoffs = cutoffs_pesr_depth, name = "pesr_depth", - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_cutoff_metrics } @@ -74,7 +74,7 @@ workflow GenotypeBatchMetrics { input: cutoffs = cutoffs_depth_pesr, name = "depth_pesr", - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_cutoff_metrics } @@ -82,7 +82,7 @@ workflow GenotypeBatchMetrics { input: cutoffs = cutoffs_depth_depth, name = "depth_depth", - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_cutoff_metrics } diff --git a/wdl/MakeCohortVcf.wdl b/wdl/MakeCohortVcf.wdl index a3b40f8e2..19c6d34d0 100644 --- a/wdl/MakeCohortVcf.wdl +++ b/wdl/MakeCohortVcf.wdl @@ -69,7 +69,6 @@ workflow MakeCohortVcf { # Module metrics parameters # Run module metrics workflow at the end - on by default Boolean? run_module_metrics - String? sv_pipeline_base_docker # required if run_module_metrics = true File? primary_contigs_list # required if run_module_metrics = true File? baseline_cluster_vcf # baseline files are optional for metrics workflow File? baseline_complex_resolve_vcf @@ -398,7 +397,6 @@ workflow MakeCohortVcf { baseline_cleaned_vcf = baseline_cleaned_vcf, primary_contigs_list=primary_contigs_list, run_module_metrics=run_module_metrics, - sv_pipeline_base_docker=sv_pipeline_base_docker, linux_docker=linux_docker, sv_base_mini_docker=sv_base_mini_docker, sv_pipeline_hail_docker=sv_pipeline_hail_docker, diff --git a/wdl/MakeCohortVcfMetrics.wdl b/wdl/MakeCohortVcfMetrics.wdl index 584f5e714..17a6d76f4 100644 --- a/wdl/MakeCohortVcfMetrics.wdl +++ b/wdl/MakeCohortVcfMetrics.wdl @@ -20,7 +20,7 @@ workflow MakeCohortVcfMetrics { File contig_list String linux_docker - String sv_pipeline_base_docker + String sv_pipeline_docker String? sv_base_mini_docker # required if not providing samples array RuntimeAttr? runtime_attr_sample_ids_from_vcf @@ -49,7 +49,7 @@ workflow MakeCohortVcfMetrics { prefix = "cluster", types = "DEL,DUP,INS,INV,CTX,CPX,BND", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_vcf_metrics } } @@ -63,7 +63,7 @@ workflow MakeCohortVcfMetrics { prefix = "cpx_resolve", types = "DEL,DUP,INS,INV,CTX,CPX,BND", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_vcf_metrics } } @@ -77,7 +77,7 @@ workflow MakeCohortVcfMetrics { prefix = "cpx_genotype", types = "DEL,DUP,INS,INV,CTX,CPX,BND", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_vcf_metrics } } @@ -90,7 +90,7 @@ workflow MakeCohortVcfMetrics { prefix = "cleaned", types = "DEL,DUP,INS,INV,CTX,CPX,BND,CNV", contig_list = contig_list, - sv_pipeline_base_docker = sv_pipeline_base_docker, + sv_pipeline_docker = sv_pipeline_docker, runtime_attr_override = runtime_attr_vcf_metrics } diff --git a/wdl/RegenotypeCNVs.wdl b/wdl/RegenotypeCNVs.wdl index 9e6f4e056..10e9bb309 100644 --- a/wdl/RegenotypeCNVs.wdl +++ b/wdl/RegenotypeCNVs.wdl @@ -8,7 +8,6 @@ workflow RegenotypeCNVs { input { String sv_base_mini_docker String sv_pipeline_docker - String sv_pipeline_base_docker String sv_pipeline_rdtest_docker Array[File] depth_vcfs File cohort_depth_vcf @@ -203,7 +202,6 @@ workflow RegenotypeCNVs { min_var_per_sample_outlier_threshold = min_var_per_sample_outlier_threshold, regeno_sample_overlap = regeno_sample_overlap, sv_pipeline_docker = sv_pipeline_docker, - sv_pipeline_base_docker = sv_pipeline_base_docker, runtime_attr_merge_list_creassess = runtime_attr_merge_list_creassess, runtime_attr_vcf2bed = runtime_attr_vcf2bed } diff --git a/wdl/SingleSampleFiltering.wdl b/wdl/SingleSampleFiltering.wdl index 0c25afb6c..50f3e5fbc 100644 --- a/wdl/SingleSampleFiltering.wdl +++ b/wdl/SingleSampleFiltering.wdl @@ -598,7 +598,7 @@ task SampleQC { input { File vcf File sample_filtering_qc_file - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -653,7 +653,7 @@ task SampleQC { memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB" disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD" bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker 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/wdl/TestUtils.wdl b/wdl/TestUtils.wdl index 407435572..7b8ff511e 100644 --- a/wdl/TestUtils.wdl +++ b/wdl/TestUtils.wdl @@ -51,7 +51,7 @@ task StandardizeVCF { String caller File contig_index Int min_size - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } RuntimeAttr runtime_default = object { @@ -79,7 +79,7 @@ task StandardizeVCF { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -92,7 +92,7 @@ task VCFMetrics { String types String prefix File contig_list - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -129,7 +129,7 @@ task VCFMetrics { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -138,7 +138,7 @@ task BAFMetrics { input { File baf_file Array[String] samples - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -169,7 +169,7 @@ task BAFMetrics { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -178,7 +178,7 @@ task SRMetrics { input { File sr_file Array[String] samples - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -209,7 +209,7 @@ task SRMetrics { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -218,7 +218,7 @@ task PEMetrics { input { File pe_file Array[String] samples - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -249,7 +249,7 @@ task PEMetrics { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -258,7 +258,7 @@ task CountsMetrics { input { File counts_file String sample_id - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -286,7 +286,7 @@ task CountsMetrics { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -295,7 +295,7 @@ task BincovMetrics { input { File bincov_matrix Array[String] samples - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -326,7 +326,7 @@ task BincovMetrics { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -336,7 +336,7 @@ task MedcovMetrics { File medcov_file Array[String] samples File? baseline_medcov_file - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -370,7 +370,7 @@ task MedcovMetrics { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -381,7 +381,7 @@ task MergedDepthMetricsWithBaseline { File baseline_bed String type File contig_list - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -419,7 +419,7 @@ task MergedDepthMetricsWithBaseline { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -429,7 +429,7 @@ task MergedDepthMetricsWithoutBaseline { File bed String type File contig_list - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -457,7 +457,7 @@ task MergedDepthMetricsWithoutBaseline { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -468,7 +468,7 @@ task MetricsFileMetrics { File contig_list Boolean common String prefix - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -498,7 +498,7 @@ task MetricsFileMetrics { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -509,7 +509,7 @@ task CutoffAndOutlierMetrics { File outlier_list File filtered_ped_file Array[String] samples - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -542,7 +542,7 @@ task CutoffAndOutlierMetrics { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -551,7 +551,7 @@ task GenotypingCutoffMetrics { input { File cutoffs String name - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } RuntimeAttr runtime_default = object { @@ -577,7 +577,7 @@ task GenotypingCutoffMetrics { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } @@ -625,7 +625,7 @@ task PlotMetrics { File test_metrics File base_metrics Array[String] samples - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -656,7 +656,7 @@ task PlotMetrics { cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb]) } } \ No newline at end of file diff --git a/wdl/TrainGCNV.wdl b/wdl/TrainGCNV.wdl index 53ea37a7d..579d1255e 100644 --- a/wdl/TrainGCNV.wdl +++ b/wdl/TrainGCNV.wdl @@ -17,7 +17,7 @@ workflow TrainGCNV { File reference_index # Index (.fai), must be in same dir as fasta File reference_dict # Dictionary (.dict), must be in same dir as fasta - # Options for subsetting samples for training. Both options require providing sv_pipeline_base_docker + # Options for subsetting samples for training. # Assumes all other inputs correspond to the full sample list. Intended for Terra Int? n_samples_subsample # Number of samples to subsample from provided sample list for trainGCNV (rec: ~100) Int subsample_seed = 42 @@ -88,7 +88,7 @@ workflow TrainGCNV { String linux_docker String gatk_docker String condense_counts_docker - String? sv_pipeline_base_docker # required if using n_samples_subsample or sample_ids_training_subset to subset samples + String? sv_pipeline_docker # required if using n_samples_subsample or sample_ids_training_subset to subset samples # Runtime configuration overrides RuntimeAttr? condense_counts_runtime_attr @@ -108,7 +108,7 @@ workflow TrainGCNV { all_strings = write_lines(samples), subset_strings = write_lines(select_first([sample_ids_training_subset])), prefix = cohort, - sv_pipeline_base_docker = select_first([sv_pipeline_base_docker]) + sv_pipeline_docker = select_first([sv_pipeline_docker]) } } @@ -119,7 +119,7 @@ workflow TrainGCNV { seed = subsample_seed, subset_size = select_first([n_samples_subsample]), prefix = cohort, - sv_pipeline_base_docker = select_first([sv_pipeline_base_docker]) + sv_pipeline_docker = select_first([sv_pipeline_docker]) } } diff --git a/wdl/Utils.wdl b/wdl/Utils.wdl index 313a25526..16efe98b9 100644 --- a/wdl/Utils.wdl +++ b/wdl/Utils.wdl @@ -214,7 +214,7 @@ task RunQC { String name File metrics File qc_definitions - String sv_pipeline_base_docker + String sv_pipeline_docker Float mem_gib = 1 Int disk_gb = 10 Int preemptible_attempts = 3 @@ -235,7 +235,7 @@ task RunQC { memory: "~{mem_gib} GiB" disks: "local-disk ~{disk_gb} HDD" bootDiskSizeGb: 10 - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker preemptible: preemptible_attempts maxRetries: 1 } @@ -248,7 +248,7 @@ task RandomSubsampleStringArray { Int seed Int subset_size String prefix - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -297,7 +297,7 @@ task RandomSubsampleStringArray { memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB" disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD" bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries]) maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries]) } @@ -308,7 +308,7 @@ task GetSubsampledIndices { File all_strings File subset_strings String prefix - String sv_pipeline_base_docker + String sv_pipeline_docker RuntimeAttr? runtime_attr_override } @@ -349,7 +349,7 @@ task GetSubsampledIndices { memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB" disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD" bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb]) - docker: sv_pipeline_base_docker + docker: sv_pipeline_docker preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries]) maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries]) }