broadinstitute/warp
Nov 2024 – Oct 2025
3 Months active
Languages Used
wdlmarkdowntextbashpython
Technical Skills
BioinformaticsGenomicsPipeline Developmentbioinformatics pipeline developmentworkflow managementBash
Farzaneh Khajouei
PROFILE
Farzaneh Khajouei
Farhad Khajoueinejad contributed to the broadinstitute/warp repository by developing and refining bioinformatics pipelines for large-scale genomics. He upgraded the Opossum Pipeline’s indexing from TBI to CSI, enabling support for large chromosomes and improving cross-pipeline compatibility. Using Python, Bash, and WDL, Farhad fixed a critical join barcode step, enhancing reliability for large genomic datasets. He also integrated MitoFinder into the BuildIndices workflow, adding optional mitochondrial data processing and annotation. Additionally, he optimized the snm3C demultiplexing workflow by refining read thresholds, which improved data quality and resource efficiency. His work emphasized maintainability, documentation, and reproducibility across workflows.
Overall Statistics
Feature vs Bugs
67%Features
Repository Contributions
3Total
Bugs
1
Commits
3
Features
2
Lines of code
369
Activity Months3
Your Network
55 people
Work 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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