Code

Integrate DRAGEN-SV into pipeline#749

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kjaisingh wants to merge 106 commits intomainbroadinstitute/gatk-sv:mainfrom kj_dragensv_benchmarkingbroadinstitute/gatk-sv:kj_dragensv_benchmarkingCopy head branch name to clipboard

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Commits

Commits on Nov 14, 2024

• Initial commit to test dockstore sync

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• Initial work - WIP

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Commits on Nov 19, 2024

• Merge branch 'main' into kj_dragensv_benchmarking

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Commits on Nov 20, 2024

• Initial implementation of DragenStandardizer

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• Added automated sync

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• Circumvented linting errors

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Commits on Nov 21, 2024

• Initialized new std_dragen file

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Commits on Nov 22, 2024

• Updated WDL & standardizer to output std_dragen_vcf

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• Resolved linting errors

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Commits on Nov 25, 2024

• Modified WDLs across workflows to integrate dragen

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• Updated WDL input params

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Commits on Nov 26, 2024

• Modified dragen_std to print

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• Modified standardizer to align with manta

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• Python linting errors

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Commits on Nov 27, 2024

• Added MATEID indexing to drop paired mates

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• Added indexing for vcf's without it

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Commits on Dec 2, 2024

• Modified vapor wdl to remove unnecessary ref inputs

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Commits on Dec 3, 2024

• Initial commit for PreprocessDragenVcf

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• Removed irrelevant inputs from vapor WDLs

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• Added OAUTH_TOKEN to localize files

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• Initial commit for CombineVcfs

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• Minor differences

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• Modified passing of arguments to SVCluster

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• Further formatting & naming changes

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• Removed /src/ from script path

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• Modified to take in fai as well

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• Added ref_dict to SVCluster call

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• Added index files

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Commits on Dec 4, 2024

• Updated combinevcf WDL syntactically

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• Added index file to output of combinevcfs

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• Updated bgzip operation to explicitly use bgzip

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• Reverted previous commit - found root of problem

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• Removed tabix from svconcordance

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• Reverted changes to vapor inputs

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Commits on Dec 6, 2024

• Removed tabix step from CombineVcfs

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• Modified pesr vcfs to dynamically use all defined but depth

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• Updated batchsamples workflow to choose pesr vcfs dynamically

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• Reverted to old version - doesn't support list comprehension

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Commits on Jan 6, 2025

• Merge branch 'main' into kj_dragensv_benchmarking

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  ed60fc0

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• Minor formatting update

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Commits on Jan 7, 2025

• Added inversion detection

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• Linting errors

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Commits on Jan 9, 2025

• Updated standardizer to mark inversions

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Commits on Jan 13, 2025

• Added INV to dragen metrics

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• Updated dragen standardizer

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Commits on Jan 15, 2025

• Temp updates - WIP

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Commits on Jan 21, 2025

• Final dragen standardizer cleanup

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  f4b502f

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• Fixed linting issues

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• Minor update to SVCluster to use variant prefix

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Commits on Jan 24, 2025

• Removed sorting from preprocessing wdl

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Commits on Jan 27, 2025

• Init commit of preprocess vcf for makegq wdl

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• Updated output fields in preprocessformakegq

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• Minor update to file path

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Commits on Jan 28, 2025

• Made localization an optional input

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• Registered branch to dockstore

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• Additional commit for dockstore.yml

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• Resolved syntax issues

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• Added branch to dockstore

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• Updated the preprocessformakegq wdl

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  fc933ac

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• Updated vapor wdl to localize crams and ignore readfilters

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• Updated standardizer

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• Removed .bam from local_bai file

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Commits on Jan 31, 2025

• Removed variant prefix from standardization WDL

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Commits on Feb 4, 2025

• Resolved merge conflicts

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• Removed redundant WDLs

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• Readding preprocess vcf for vapor

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• Added project ID for vapor WDL

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Commits on Feb 5, 2025

• Modified other files that reference manta to include dragen

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• Removed line spacing

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Commits on Feb 7, 2025

• Integrated new params into makegq/concordance workflow

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• Restructured representation of track_intervals/track_name

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• Renamed task param

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• Misspelt track_names variable

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• Added MakeGq to dockstore sync

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• Additional commit to trigger docker sync

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Commits on Feb 10, 2025

• Updated MakeGq to pass max_cnv_size to RefineSampleLabels

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• Modified prep sample vcf script to include max size limit param

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Commits on Feb 12, 2025

• Drop --do-not-sort

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• Added space between track name/intervals params

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Commits on Feb 13, 2025

• Re-add standardization wdl

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• Added CNV standardizer

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• Renmaed vcf to tabix

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Commits on Feb 16, 2025

• Rearranged wdl structure in makebincovmatrix

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Commits on Feb 18, 2025

• Created wdls to extract filter values into json

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• Added sample IDs to filter extraction workflow

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• Removed extra version tag

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• Readded subsetvcfbysamples

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• Replaced bash code with python for extractfilters

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• Resolved missing variable in python command block

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• Updated python code

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• Added closing CODE value

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Commits on Feb 20, 2025

• Updated cnv standardizer + filterbatchsites to take optional scores input

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• Initial commit of SVConcordanceSimple

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• Conditionally call FilterBatchSites if inputs don't exist

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• Minor update to concordance WDL

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• Included idx in concordance wdl

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Commits on Feb 22, 2025

• Added depth params to makegq/svconcordancepbsample

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Commits on Feb 23, 2025

• Updated standardizer to modify genotypes

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• Updated cnv standardizer

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Commits on Feb 24, 2025

• Updated MakeGq to take in mixed overlap params

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• Revived combinevcfs task

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Commits on Feb 25, 2025

• Created WDL to extract qual

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• Updated two WDLs for processing data

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Commits on Feb 26, 2025

• Create wdl for region exclusion

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Commits on Feb 27, 2025

• Fixed ends for interchromosal events in svtk vcfcluster

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Commits on Mar 10, 2025

• FilterBatchSites - skip RewriteScores if overriden

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