Code

Integrate DRAGEN-SV into pipeline#749

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kjaisingh wants to merge 68 commits intomainbroadinstitute/gatk-sv:mainfrom kj_dragensv_benchmarkingbroadinstitute/gatk-sv:kj_dragensv_benchmarkingCopy head branch name to clipboard

+751-160

Commits

Commits on Nov 14, 2024

• Initial commit to test dockstore sync

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  e823d20

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• Initial work - WIP

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  6127ef1

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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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  40b7fb5

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Commits on Nov 25, 2024

• Modified WDLs across workflows to integrate dragen

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  9c457d1

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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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  9897ed0

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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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  4fa2ba2

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• Minor differences

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  d7f6ada

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• Modified passing of arguments to SVCluster

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  8134dc6

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• Further formatting & naming changes

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• Removed /src/ from script path

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  0327cc8

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• Modified to take in fai as well

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  e595de0

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• Added ref_dict to SVCluster call

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  5876c27

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• Added index files

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Commits on Dec 4, 2024

• Updated combinevcf WDL syntactically

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  0d2c9fb

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• Added index file to output of combinevcfs

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  1ff0ad2

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• Updated bgzip operation to explicitly use bgzip

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  f2f1da4

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• Reverted previous commit - found root of problem

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  9d6cbd4

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• Removed tabix from svconcordance

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  30e1cb6

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• Reverted changes to vapor inputs

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  4a27320

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Commits on Dec 6, 2024

• Removed tabix step from CombineVcfs

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  06d5f1c

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• Modified pesr vcfs to dynamically use all defined but depth

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  d6a13a2

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• Updated batchsamples workflow to choose pesr vcfs dynamically

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  5c778d4

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

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  c6cdf40

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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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  aba4ba4

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Commits on Jan 7, 2025

• Added inversion detection

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  a61a342

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• Linting errors

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  9079a3b

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Commits on Jan 9, 2025

• Updated standardizer to mark inversions

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  395d519

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Commits on Jan 13, 2025

• Added INV to dragen metrics

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  416d459

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• Updated dragen standardizer

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  ba12de1

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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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  ab505fd

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• Minor update to SVCluster to use variant prefix

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  3fb7a1b

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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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  55bb2b6

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• Updated output fields in preprocessformakegq

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• Minor update to file path

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  06e3a6c

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Commits on Jan 28, 2025

• Made localization an optional input

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  52ef8a1

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• Registered branch to dockstore

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• Additional commit for dockstore.yml

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  902b4e9

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• Resolved syntax issues

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  5ee1d60

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• Added branch to dockstore

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  7d4266b

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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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  1ec076b

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• Updated standardizer

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  16e89fb

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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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  9c598ad

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• Removed redundant WDLs

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  bdb3bcc

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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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