broadinstitute/warp
Nov 2024 – Oct 2025
3 Months active
Languages Used
wdlmarkdowntextbashpython
Technical Skills
BioinformaticsGenomicsPipeline Developmentbioinformatics pipeline developmentworkflow managementBash
Farzaneh Khajouei
PROFILE
Farzaneh Khajouei
Contributed to the broadinstitute/warp repository by developing and refining bioinformatics pipelines focused on genomics data processing. Over three months, implemented features such as optional mitochondrial data support in the BuildIndices WDL using Bash, Python, and WDL, integrating MitoFinder for enhanced annotation workflows. Improved the snm3C demultiplexing pipeline by tuning read thresholds to optimize data quality and resource usage. Addressed scalability in the Opossum Pipeline by upgrading Tabix indexing from TBI to CSI, enabling support for large chromosomes and fixing a critical join barcode step. Maintained robust documentation, versioning, and changelogs to ensure reproducibility and cross-pipeline compatibility.
Overall Statistics
Feature vs Bugs
67%Features
Repository Contributions
3Total
Bugs
1
Commits
3
Features
2
Lines of code
369
Activity Months3
Your Network
63 peopleWork History
October 2025
1 Commits • 1 Features
Oct 1, 2025October 2025: Implemented optional mitochondrial data support in the BuildIndices WDL for broadinstitute/warp by integrating MitoFinder, enabling optional appending of mitochondrial sequences and annotations. Added dedicated tasks for mitochondrial annotation and GTF merging, updated pipeline versions and changelogs, and prepared the workflow to process mitochondrial data end-to-end.
1 Commits • 1 Features
Oct 1, 2025October 2025: Implemented optional mitochondrial data support in the BuildIndices WDL for broadinstitute/warp by integrating MitoFinder, enabling optional appending of mitochondrial sequences and annotations. Added dedicated tasks for mitochondrial annotation and GTF merging, updated pipeline versions and changelogs, and prepared the workflow to process mitochondrial data end-to-end.
October 2025
August 2025
1 Commits • 1 Features
Aug 1, 2025Monthly summary for 2025-08 (broadinstitute/warp): Focused on quality improvement and reproducibility of the snm3C demultiplexing workflow. Delivered a targeted feature refinement that reduces the read threshold to better match typical sample loads, and updated the pipeline version and changelog to ensure traceability. No major bugs fixed this month. Impact: higher-quality demultiplexed data, reduced compute/resource usage, and faster, more reliable downstream analyses. Technologies demonstrated: WDL pipeline tuning, versioning and changelog practices, commit traceability, and cross-team collaboration.
August 2025
1 Commits • 1 Features
Aug 1, 2025Monthly summary for 2025-08 (broadinstitute/warp): Focused on quality improvement and reproducibility of the snm3C demultiplexing workflow. Delivered a targeted feature refinement that reduces the read threshold to better match typical sample loads, and updated the pipeline version and changelog to ensure traceability. No major bugs fixed this month. Impact: higher-quality demultiplexed data, reduced compute/resource usage, and faster, more reliable downstream analyses. Technologies demonstrated: WDL pipeline tuning, versioning and changelog practices, commit traceability, and cross-team collaboration.
November 2024
1 Commits
Nov 1, 2024November 2024 focused on stabilizing and scaling the Opossum Pipeline in broadinstitute/warp. Delivered indexing upgrade from TBI to CSI to support large-chromosome data and updated pipeline versions and changelogs across related pipelines. Fixed a critical join barcode step issue, improving reliability when processing large genomic datasets and ensuring cross-pipeline compatibility. Coordinated with multiple repos to align versions and documentation, reducing downstream maintenance.
1 Commits
Nov 1, 2024November 2024 focused on stabilizing and scaling the Opossum Pipeline in broadinstitute/warp. Delivered indexing upgrade from TBI to CSI to support large-chromosome data and updated pipeline versions and changelogs across related pipelines. Fixed a critical join barcode step issue, improving reliability when processing large genomic datasets and ensuring cross-pipeline compatibility. Coordinated with multiple repos to align versions and documentation, reducing downstream maintenance.
November 2024
Activity
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Quality Metrics
Correctness83.4%
Maintainability80.0%
Architecture83.4%
Performance80.0%
AI Usage36.6%
Skills & Technologies
Programming Languages
bashmarkdownpythontextwdl
Technical Skills
BashBioinformaticsGenomicsPipeline DevelopmentPythonWDLbioinformaticsbioinformatics pipeline developmentscriptingworkflow managementworkflow orchestration
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