From 80e09798225912760de88856f84fe79dec389f09 Mon Sep 17 00:00:00 2001 From: cwhelan Date: Tue, 30 Jun 2020 10:57:14 -0400 Subject: [PATCH] Fix running without any MELT inputs (#6) * update wdl to make melt ref panel inputs truly optional * create an input file to demonstrate running without melt * fix typo in delly filtering stanza --- ...eSample.ref_panel_1kg.na12878.no_melt.json | 1175 +++++++++++++++++ wdl/GATKSVPipelineSingleSample.wdl | 67 +- 2 files changed, 1219 insertions(+), 23 deletions(-) create mode 100644 inputs/GATKSVPipelineSingleSample.ref_panel_1kg.na12878.no_melt.json diff --git a/inputs/GATKSVPipelineSingleSample.ref_panel_1kg.na12878.no_melt.json b/inputs/GATKSVPipelineSingleSample.ref_panel_1kg.na12878.no_melt.json new file mode 100644 index 000000000..a2b496888 --- /dev/null +++ b/inputs/GATKSVPipelineSingleSample.ref_panel_1kg.na12878.no_melt.json @@ -0,0 +1,1175 @@ +{ + "GATKSVPipelineSingleSample.sample_id" : "NA12878", + "GATKSVPipelineSingleSample.batch" : 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"gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-83.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-84.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-85.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-86.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-87.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-88.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-89.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-9.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-90.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-91.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-92.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-93.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-94.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-95.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-96.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-97.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-98.tar.gz", + "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-99.tar.gz" + ] +} diff --git a/wdl/GATKSVPipelineSingleSample.wdl b/wdl/GATKSVPipelineSingleSample.wdl index e96089568..19c267ec8 100644 --- a/wdl/GATKSVPipelineSingleSample.wdl +++ b/wdl/GATKSVPipelineSingleSample.wdl @@ -240,7 +240,7 @@ workflow GATKSVPipelineSingleSample { # Reference panel standardized caller VCFs Array[File] ref_std_manta_vcfs Array[File] ref_std_wham_vcfs - Array[File] ref_std_melt_vcfs + Array[File]? ref_std_melt_vcfs File ref_panel_del_bed File ref_panel_dup_bed @@ -581,7 +581,10 @@ workflow GATKSVPipelineSingleSample { # Merge calls with reference panel Array[File] merged_manta_vcfs_array = flatten([select_first([Module00c.std_manta_vcf]), ref_std_manta_vcfs]) Array[File] merged_wham_vcfs_array = flatten([select_first([Module00c.std_wham_vcf]), ref_std_wham_vcfs]) - Array[File] merged_melt_vcfs_array = flatten([select_first([Module00c.std_melt_vcf]), ref_std_melt_vcfs]) + if (defined(Module00c.std_melt_vcf)) { + Array[File]? merged_melt_vcfs_array = flatten([select_first([Module00c.std_melt_vcf]), select_first([ref_std_melt_vcfs])]) + } + call dpn.MergeSet as MergeSetDel { input: beds=[Module00c.merged_dels, ref_panel_del_bed], @@ -628,30 +631,47 @@ workflow GATKSVPipelineSingleSample { } # Pull out clustered calls from this sample only - call SingleSampleFiltering.FilterVcfBySampleGenotypeAndAddEvidenceAnnotation as FilterManta { - input : - vcf_gz=select_first([Module01.manta_vcf]), - sample_id=sample_id, - evidence="RD,PE,SR", - sv_base_mini_docker=sv_base_mini_docker, - runtime_attr_override=runtime_attr_filter_vcf_by_id + if (use_manta) { + call SingleSampleFiltering.FilterVcfBySampleGenotypeAndAddEvidenceAnnotation as FilterManta { + input : + vcf_gz=select_first([Module01.manta_vcf]), + sample_id=sample_id, + evidence="RD,PE,SR", + sv_base_mini_docker=sv_base_mini_docker, + runtime_attr_override=runtime_attr_filter_vcf_by_id + } } - call SingleSampleFiltering.FilterVcfBySampleGenotypeAndAddEvidenceAnnotation as FilterWham { - input : - vcf_gz=select_first([Module01.wham_vcf]), - sample_id=sample_id, - evidence="RD,PE,SR", - sv_base_mini_docker=sv_base_mini_docker, - runtime_attr_override=runtime_attr_filter_vcf_by_id + if (use_wham) { + call SingleSampleFiltering.FilterVcfBySampleGenotypeAndAddEvidenceAnnotation as FilterWham { + input : + vcf_gz=select_first([Module01.wham_vcf]), + sample_id=sample_id, + evidence="RD,PE,SR", + sv_base_mini_docker=sv_base_mini_docker, + runtime_attr_override=runtime_attr_filter_vcf_by_id + } } - call SingleSampleFiltering.FilterVcfBySampleGenotypeAndAddEvidenceAnnotation as FilterMelt { - input : - vcf_gz=select_first([Module01.melt_vcf]), - sample_id=sample_id, - evidence="RD,PE,SR", - sv_base_mini_docker=sv_base_mini_docker, - runtime_attr_override=runtime_attr_filter_vcf_by_id + if (use_melt) { + call SingleSampleFiltering.FilterVcfBySampleGenotypeAndAddEvidenceAnnotation as FilterMelt { + input : + vcf_gz=select_first([Module01.melt_vcf]), + sample_id=sample_id, + evidence="RD,PE,SR", + sv_base_mini_docker=sv_base_mini_docker, + runtime_attr_override=runtime_attr_filter_vcf_by_id + } + } + if (use_delly) { + call SingleSampleFiltering.FilterVcfBySampleGenotypeAndAddEvidenceAnnotation as FilterDelly { + input : + vcf_gz=select_first([Module01.delly_vcf]), + sample_id=sample_id, + evidence="RD,PE,SR", + sv_base_mini_docker=sv_base_mini_docker, + runtime_attr_override=runtime_attr_filter_vcf_by_id + } } + call SingleSampleFiltering.FilterVcfBySampleGenotypeAndAddEvidenceAnnotation as FilterDepth { input : vcf_gz=Module01.depth_vcf, @@ -666,6 +686,7 @@ workflow GATKSVPipelineSingleSample { manta_vcf=FilterManta.out, wham_vcf=FilterWham.out, melt_vcf=FilterMelt.out, + delly_vcf=FilterDelly.out, batch=batch, sv_base_mini_docker=sv_base_mini_docker, runtime_attr_override=runtime_attr_merge_pesr_vcfs