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broadinstitute / gatk-sv Public

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Add check for duplicate records to MainVcfQc#705

Merged

kjaisingh merged 31 commits intomainbroadinstitute/gatk-sv:mainfrom kj/701_vcf_qc_duplicatesbroadinstitute/gatk-sv:kj/701_vcf_qc_duplicatesCopy head branch name to clipboard

Oct 28, 2024

+328

Conversation Commits31 (31)Checks Files changed

Commits

Commits on Aug 6, 2024

Initial commit
kjaisingh
committed
Added branch name to dockstore file
kjaisingh
committed
Updated script definitions
kjaisingh
committed
Updated WDL to use custom script
kjaisingh
committed

Commits on Aug 7, 2024

Modified output file paths
kjaisingh
committed
Added more logging
kjaisingh
committed
Used dot notation
kjaisingh
committed
Minor logging changes
kjaisingh
committed
Removed glob() references
kjaisingh
committed
Standardized variable input structure
kjaisingh
committed
Removed direct python script call
kjaisingh
committed
Renamed output files to be duplicate instead of duplicated
kjaisingh
committed
Removed call to MergeDuplicates
kjaisingh
committed
Undo commenting out of MergeDuplicates
kjaisingh
committed

Commits on Aug 8, 2024

Removed direct reference to vcfs_for_qc
kjaisingh
committed
Minor changes
kjaisingh
committed

Commits on Aug 9, 2024

Added option for both default and custom script
kjaisingh
committed
Modified path to python scripts
kjaisingh
committed
Removed unused import
kjaisingh
committed
Resoled all flake8 linting errors
kjaisingh
committed
Rolled back to solely use custom scripts for time being
kjaisingh
committed

Commits on Sep 25, 2024

Update wdl/MainVcfQc.wdl

kjaisingh
and
mwalker174
authored
Updated files
kjaisingh
committed
Merge branch 'kj/701_vcf_qc_duplicates' of https://github.com/broadinstitute/gatk-sv into kj/701_vcf_qc_duplicates
kjaisingh
committed
Merge branch 'main' into kj/701_vcf_qc_duplicates
kjaisingh
committed

Commits on Sep 26, 2024

Re-added extra line
kjaisingh
committed
Corrected line add to test docker image publishing
kjaisingh
committed
Corrected to use identify_duplicates in task
kjaisingh
committed
Added root path for python files
kjaisingh
committed
Minor script update - use lowercase exact
kjaisingh
committed
Removed dockstore push
kjaisingh
committed

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