broadinstitute/warp
Nov 2024 – Oct 2025
7 Months active
Languages Used
MarkdownmdwdlPythonShellWDLYAMLmarkdown
Technical Skills
Documentationpipeline configurationversion controlworkflow managementCloud Computing (GCP)Data Engineering
Jessica Way
PROFILE
Jessica Way
Over seven months, Jway contributed to the broadinstitute/warp repository by developing and refining genomic data processing pipelines, with a focus on automation, reproducibility, and cloud scalability. Jway implemented features such as region-based variant filtering, per-chromosome VCF generation, and mitochondrial DNA analysis, leveraging technologies like WDL, Python, and Google Cloud. Their work included integrating pipelines with Dockstore, enhancing documentation for user onboarding, and standardizing output naming and versioning to improve traceability. By addressing workflow orchestration and batch processing reliability, Jway enabled more efficient, scalable analyses for large genomic cohorts, demonstrating depth in bioinformatics pipeline engineering and cloud-native workflow management.
Overall Statistics
Feature vs Bugs
90%Features
Repository Contributions
12Total
Bugs
1
Commits
12
Features
9
Lines of code
12,791
Activity Months7
Your Network
55 people
Work History
October 2025
2 Commits • 2 Features
Oct 1, 2025October 2025 — Warp: Key feature work and quality improvements focused on documentation and standardized processing. Delivered: - Mitochondria Pipeline Documentation Enhancements: README improvements and fixed minor typos in changelogs for ATAC and Multiome pipelines. - Variant Filtering and QC Pipeline – v9 Update: WDL/script updates to reflect v9 processing, including call rate thresholds, dropped fields, new filter definitions, version bump, and extended worker TTL. Major bugs fixed: none identified as major; minor typo corrections completed in changelogs. Impact and value: - Improves reproducibility and onboarding via better docs, and aligns processing to v9 standards, improving data quality and reliability. - Extended worker TTL reduces job timeouts and improves throughput. - Demonstrates proficiency with WDL, pipeline scripting, and documentation tooling.
2 Commits • 2 Features
Oct 1, 2025October 2025 — Warp: Key feature work and quality improvements focused on documentation and standardized processing. Delivered: - Mitochondria Pipeline Documentation Enhancements: README improvements and fixed minor typos in changelogs for ATAC and Multiome pipelines. - Variant Filtering and QC Pipeline – v9 Update: WDL/script updates to reflect v9 processing, including call rate thresholds, dropped fields, new filter definitions, version bump, and extended worker TTL. Major bugs fixed: none identified as major; minor typo corrections completed in changelogs. Impact and value: - Improves reproducibility and onboarding via better docs, and aligns processing to v9 standards, improving data quality and reliability. - Extended worker TTL reduces job timeouts and improves throughput. - Demonstrates proficiency with WDL, pipeline scripting, and documentation tooling.
October 2025
August 2025
5 Commits • 3 Features
Aug 1, 2025August 2025: Expanded Warp's genomic workflow suite with mitochondria-focused pipelines integrated into Dockstore, introduced a PCA analysis pipeline for unlabeled genomic data, and added an optional aligned ATAC BAM input to skip explicit alignment across ATAC, Multiome, and PairedTag workflows. These deliverables broaden analysis coverage, reduce unnecessary processing, and improve deployment reproducibility through Dockstore exposure and versioned changes. No critical defects were reported; staging promotions and tool-version updates improved reliability and traceability. Technologies demonstrated include WDL, Dockstore integration, BGZ VCF processing, HWE-normalized PCA with visualization, and ATAC/Multiome/PairedTag orchestration, with cross-domain enhancements for mtDNA, HLA genotyping, and QC workflows.
August 2025
5 Commits • 3 Features
Aug 1, 2025August 2025: Expanded Warp's genomic workflow suite with mitochondria-focused pipelines integrated into Dockstore, introduced a PCA analysis pipeline for unlabeled genomic data, and added an optional aligned ATAC BAM input to skip explicit alignment across ATAC, Multiome, and PairedTag workflows. These deliverables broaden analysis coverage, reduce unnecessary processing, and improve deployment reproducibility through Dockstore exposure and versioned changes. No critical defects were reported; staging promotions and tool-version updates improved reliability and traceability. Technologies demonstrated include WDL, Dockstore integration, BGZ VCF processing, HWE-normalized PCA with visualization, and ATAC/Multiome/PairedTag orchestration, with cross-domain enhancements for mtDNA, HLA genotyping, and QC workflows.
July 2025
1 Commits • 1 Features
Jul 1, 2025July 2025: Delivered targeted region-based variant filtering and QC for AoU VCF in broadinstitute/warp. Added optional start and end position arguments to the Python script and WDL workflow to enable region-restricted filtering and QC, refining variant selection with adjusted filtering thresholds. This work improves data quality for AoU analyses, enables precise, region-specific cohort processing, and lays groundwork for scalable, reproducible AoU data handling. Committed as 28525075a4f2671bf3eeed650affa757fe7d596e with message 'Jw subset aou vcf by region (#1626)'.
1 Commits • 1 Features
Jul 1, 2025July 2025: Delivered targeted region-based variant filtering and QC for AoU VCF in broadinstitute/warp. Added optional start and end position arguments to the Python script and WDL workflow to enable region-restricted filtering and QC, refining variant selection with adjusted filtering thresholds. This work improves data quality for AoU analyses, enables precise, region-specific cohort processing, and lays groundwork for scalable, reproducible AoU data handling. Committed as 28525075a4f2671bf3eeed650affa757fe7d596e with message 'Jw subset aou vcf by region (#1626)'.
July 2025
June 2025
1 Commits
Jun 1, 2025June 2025: Stabilized the Snm3C pipeline batch processing in Warp for Google Batch, delivering a reliability fix and ensuring future compatibility. Key changes include updating the cromwell_root_dir default to align with Google Batch requirements, bumping the Snm3C pipeline version, and refreshing the changelog to document the change. Result: improved reliability and scalability of Snm3C workflows on Google Cloud with maintainable versioning.
June 2025
1 Commits
Jun 1, 2025June 2025: Stabilized the Snm3C pipeline batch processing in Warp for Google Batch, delivering a reliability fix and ensuring future compatibility. Key changes include updating the cromwell_root_dir default to align with Google Batch requirements, bumping the Snm3C pipeline version, and refreshing the changelog to document the change. Result: improved reliability and scalability of Snm3C workflows on Google Cloud with maintainable versioning.
May 2025
1 Commits • 1 Features
May 1, 2025May 2025 monthly summary for broadinstitute/warp development. Focused on delivering the Genomic Variant QC Pipeline and Per-Chromosome VCF Generation feature, enabling scalable quality control of genomic variants on cloud infrastructure. Implemented a Hail-based QC pipeline with a WDL workflow to orchestrate execution on Google Cloud Dataproc, and added per-chromosome VCF generation accompanied by detailed QC reports. This work enhances automation, reproducibility, and scalability of genomic QC, while reducing manual intervention in downstream analysis.
1 Commits • 1 Features
May 1, 2025May 2025 monthly summary for broadinstitute/warp development. Focused on delivering the Genomic Variant QC Pipeline and Per-Chromosome VCF Generation feature, enabling scalable quality control of genomic variants on cloud infrastructure. Implemented a Hail-based QC pipeline with a WDL workflow to orchestrate execution on Google Cloud Dataproc, and added per-chromosome VCF generation accompanied by detailed QC reports. This work enhances automation, reproducibility, and scalability of genomic QC, while reducing manual intervention in downstream analysis.
May 2025
January 2025
1 Commits • 1 Features
Jan 1, 2025January 2025 — Broad Institute Warp: Delivered versioning and output-name standardization across the ReblockGVCF workflow and related pipelines, with changelog updates and coordinated version bumps across ReblockGVCF, UltimaGenomicsWholeGenomeGermline, and BroadInternalUltimaGenomics. This work improves reproducibility, traceability, and downstream automation across the pipeline suite.
January 2025
1 Commits • 1 Features
Jan 1, 2025January 2025 — Broad Institute Warp: Delivered versioning and output-name standardization across the ReblockGVCF workflow and related pipelines, with changelog updates and coordinated version bumps across ReblockGVCF, UltimaGenomicsWholeGenomeGermline, and BroadInternalUltimaGenomics. This work improves reproducibility, traceability, and downstream automation across the pipeline suite.
November 2024
1 Commits • 1 Features
Nov 1, 2024November 2024 — Focused on improving documentation and discoverability for the snM3C pipeline in broadinstitute/warp. Key feature delivered: added a new Documentation entry for Summary_PerCellOutput in the README's docs table, describing a custom bash function used to untar files at a per-cell level, improving discoverability of this capability. Committed change documented in the repo history. Major bugs fixed: none reported this period. Overall impact: enhanced developer and user onboarding, enabling faster adoption of per-cell untar workflows and reducing support overhead. Technologies/skills demonstrated: documentation best practices, clear commit messaging, and README-driven UX improvements within a collaborative repository.
1 Commits • 1 Features
Nov 1, 2024November 2024 — Focused on improving documentation and discoverability for the snM3C pipeline in broadinstitute/warp. Key feature delivered: added a new Documentation entry for Summary_PerCellOutput in the README's docs table, describing a custom bash function used to untar files at a per-cell level, improving discoverability of this capability. Committed change documented in the repo history. Major bugs fixed: none reported this period. Overall impact: enhanced developer and user onboarding, enabling faster adoption of per-cell untar workflows and reducing support overhead. Technologies/skills demonstrated: documentation best practices, clear commit messaging, and README-driven UX improvements within a collaborative repository.
November 2024
Activity
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Quality Metrics
Correctness90.0%
Maintainability88.4%
Architecture90.0%
Performance81.6%
AI Usage20.0%
Skills & Technologies
Programming Languages
MarkdownPythonShellWDLYAMLbashmarkdownmdpythonr
Technical Skills
BioinformaticsBioinformatics PipelinesCI/CDCloud ComputingCloud Computing (GCP)Data AnalysisData EngineeringData ProcessingDevOpsDockerDocumentationGenomic Data ProcessingGenomicsHailPCA
Repositories Contributed To
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