broadinstitute/warp
Dec 2025 – Dec 2025
1 Month active
Languages Used
WDLbash
Technical Skills
bioinformaticsdata processinggenome analysisgenome processinggenomic analysispipeline development
npetrill
PROFILE
Npetrill
During December 2025, Nick Petrillo enhanced genome data preparation workflows in the broadinstitute/warp repository, focusing on improving reliability and reproducibility for downstream analyses. He addressed duplicate contig issues in FASTA files to ensure accurate genome indexing with bwa-mem2 and refined GTF processing by filtering out lines with 'source' in the third column, which improved STAR index quality. Nick also implemented dynamic handling of mitochondrial accessions, conditionally removing duplicate contigs to stabilize data preparation for both indexing and STAR workflows. His work demonstrated depth in bioinformatics, data processing, and scripting, utilizing WDL, bash, and Python to deliver robust pipeline improvements.
Overall Statistics
Feature vs Bugs
67%Features
Repository Contributions
11Total
Bugs
1
Commits
11
Features
2
Lines of code
196
Activity Months1
Your Network
58 peopleWork History
December 2025
11 Commits • 2 Features
Dec 1, 2025December 2025 monthly summary for broadinstitute/warp. Focused on robust genome data prep and indexing improvements to reduce errors and improve downstream analyses. Delivered three primary updates: 1) remove duplicate contig NC_028718.1 from FASTA prior to genome indexing (bwa-mem2) to ensure accurate indexing; 2) enhance GTF processing for STAR index build by removing lines where third column is 'source', improving index quality; 3) dynamic mitochondrial accession handling with conditional removal of duplicate contigs to stabilize genome data preparation for indexing and STAR workflows. Impact: reduces indexing failures, improves alignment reliability and reproducibility, and provides clearer changelogs for audit and collaboration. Technologies demonstrated: bwa-mem2, STAR, GTF cleaning, dynamic data handling, changelog maintenance, Python scripting.
11 Commits • 2 Features
Dec 1, 2025December 2025 monthly summary for broadinstitute/warp. Focused on robust genome data prep and indexing improvements to reduce errors and improve downstream analyses. Delivered three primary updates: 1) remove duplicate contig NC_028718.1 from FASTA prior to genome indexing (bwa-mem2) to ensure accurate indexing; 2) enhance GTF processing for STAR index build by removing lines where third column is 'source', improving index quality; 3) dynamic mitochondrial accession handling with conditional removal of duplicate contigs to stabilize genome data preparation for indexing and STAR workflows. Impact: reduces indexing failures, improves alignment reliability and reproducibility, and provides clearer changelogs for audit and collaboration. Technologies demonstrated: bwa-mem2, STAR, GTF cleaning, dynamic data handling, changelog maintenance, Python scripting.
December 2025
Activity
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Quality Metrics
Correctness92.8%
Maintainability85.4%
Architecture85.4%
Performance85.4%
AI Usage21.8%
Skills & Technologies
Programming Languages
WDLbash
Technical Skills
bioinformaticsdata processinggenome analysisgenome processinggenomic analysispipeline developmentscriptingworkflow developmentworkflow management
Repositories Contributed To
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