hartwigmedical/scripts
Nov 2024 – Sep 2025
9 Months active
Languages Used
PerlRShelljqbashBashJSONPython
Technical Skills
API IntegrationCloud StorageData ProcessingFile HandlingFile ManagementScripting
Yannick Bijl
PROFILE
Yannick Bijl
Yorick Bijl developed and maintained data processing and automation workflows in the hartwigmedical/scripts repository, focusing on bioinformatics and laboratory data management. He engineered robust solutions for LIMS and LAMA API integration, streamlined sequencing and QC pipelines, and enhanced data conversion and reporting processes. Using Python, Bash, and R, Yorick implemented features such as adapter conflict detection, run registration automation, and dynamic QC trend reporting, while also addressing workflow stability and resource optimization. His work demonstrated depth through careful error handling, maintainable code structure, and proactive testing, resulting in reliable, scalable pipelines that improved data integrity and operational efficiency.
Overall Statistics
Feature vs Bugs
77%Features
Repository Contributions
64Total
Bugs
6
Commits
64
Features
20
Lines of code
1,434
Activity Months9
Your Network
57 peopleSame Organization
@hartwigmedicalfoundation.nl29
Work History
September 2025
25 Commits • 6 Features
Sep 1, 2025September 2025: Delivered substantial enhancements to hartwigmedical/scripts, increasing processing reliability, usability, and maintainability. Implemented LAMA-based results formatting and registration workflows for HSS and Run (replacing LIMS), improved script discoverability and paths, hardened data extraction from samplesheets with output checks, and fixed critical ordering and stability issues. Expanded testing infrastructure to support ongoing quality.
25 Commits • 6 Features
Sep 1, 2025September 2025: Delivered substantial enhancements to hartwigmedical/scripts, increasing processing reliability, usability, and maintainability. Implemented LAMA-based results formatting and registration workflows for HSS and Run (replacing LIMS), improved script discoverability and paths, hardened data extraction from samplesheets with output checks, and fixed critical ordering and stability issues. Expanded testing infrastructure to support ongoing quality.
September 2025
August 2025
1 Commits • 1 Features
Aug 1, 2025August 2025 monthly summary for hartwigmedical/scripts: Delivered a focused cleanup of the LIMS synchronization workflow by removing 2023 data handling and consolidating processing to current and 2024 data. This reduces obsolete code paths, simplifies maintenance, and lowers the risk of data-path regressions in production syncs.
August 2025
1 Commits • 1 Features
Aug 1, 2025August 2025 monthly summary for hartwigmedical/scripts: Delivered a focused cleanup of the LIMS synchronization workflow by removing 2023 data handling and consolidating processing to current and 2024 data. This reduces obsolete code paths, simplifies maintenance, and lowers the risk of data-path regressions in production syncs.
July 2025
1 Commits • 1 Features
Jul 1, 2025July 2025: Delivered a targeted feature to strengthen sequencing workflow reliability by adding an Adapter Conflict Detection Tool. The new Python script checks for potential conflicts between adapter sequences by computing pairwise Hamming distances and reporting pairs that fall below a defined threshold, enabling proactive validation before experiments.
1 Commits • 1 Features
Jul 1, 2025July 2025: Delivered a targeted feature to strengthen sequencing workflow reliability by adding an Adapter Conflict Detection Tool. The new Python script checks for potential conflicts between adapter sequences by computing pairwise Hamming distances and reporting pairs that fall below a defined threshold, enabling proactive validation before experiments.
July 2025
June 2025
10 Commits • 2 Features
Jun 1, 2025June 2025 monthly summary for hartwigmedical/scripts focused on delivering substantial QC enhancements and data collection tooling that improve monitoring accuracy, trend analysis, and data-driven decision-making. The work emphasizes business value through richer reporting, automated data collection, and reliable data availability for stakeholders. Key outcomes include expanded QC trends reporting with run-level metrics, a new run_qc_info datatable, a Bash script to collect QC data from collection runs, and robust data handling and plotting improvements. Technologies used include R Markdown, R data wrangling, ggplot2 visuals, Bash scripting, and cloud storage uploads for trend analysis.
June 2025
10 Commits • 2 Features
Jun 1, 2025June 2025 monthly summary for hartwigmedical/scripts focused on delivering substantial QC enhancements and data collection tooling that improve monitoring accuracy, trend analysis, and data-driven decision-making. The work emphasizes business value through richer reporting, automated data collection, and reliable data availability for stakeholders. Key outcomes include expanded QC trends reporting with run-level metrics, a new run_qc_info datatable, a Bash script to collect QC data from collection runs, and robust data handling and plotting improvements. Technologies used include R Markdown, R data wrangling, ggplot2 visuals, Bash scripting, and cloud storage uploads for trend analysis.
May 2025
4 Commits • 3 Features
May 1, 2025May 2025 monthly performance summary for hartwigmedical/scripts. Focused on precision in shallow QC tumor purity reporting, workflow simplification, and resource optimization across tumor DNA isolation. Emphasized business value: accurate LAMA API data, reduced data movement, and improved operational efficiency.
4 Commits • 3 Features
May 1, 2025May 2025 monthly performance summary for hartwigmedical/scripts. Focused on precision in shallow QC tumor purity reporting, workflow simplification, and resource optimization across tumor DNA isolation. Emphasized business value: accurate LAMA API data, reduced data movement, and improved operational efficiency.
May 2025
March 2025
8 Commits • 2 Features
Mar 1, 2025March 2025 monthly summary focusing on key accomplishments and business impact. Delivered two primary feature sets with accompanying reliability improvements in data ingestion pipelines. LAMA integration was extended and streamlined, while the HAWE-aligned Cram2fastq workflow was enhanced for naming, storage, barcode handling, and efficiency. Cleanup of obsolete scripts reduced maintenance burden and future risk. Overall, improved end-to-end data availability, traceability, and developer productivity.
March 2025
8 Commits • 2 Features
Mar 1, 2025March 2025 monthly summary focusing on key accomplishments and business impact. Delivered two primary feature sets with accompanying reliability improvements in data ingestion pipelines. LAMA integration was extended and streamlined, while the HAWE-aligned Cram2fastq workflow was enhanced for naming, storage, barcode handling, and efficiency. Cleanup of obsolete scripts reduced maintenance burden and future risk. Overall, improved end-to-end data availability, traceability, and developer productivity.
February 2025
1 Commits
Feb 1, 2025February 2025 performance summary for hartwigmedical/scripts: focused on stability and reliability of the RTG-based evaluation workflow. Implemented a memory cap for the RTGtools vcfeval step to prevent out-of-memory errors, reducing pipeline failures and enabling more consistent throughput under heavier workloads.
1 Commits
Feb 1, 2025February 2025 performance summary for hartwigmedical/scripts: focused on stability and reliability of the RTG-based evaluation workflow. Implemented a memory cap for the RTGtools vcfeval step to prevent out-of-memory errors, reducing pipeline failures and enabling more consistent throughput under heavier workloads.
February 2025
December 2024
6 Commits • 3 Features
Dec 1, 20242024-12 monthly summary for hartwigmedical/scripts: Delivered automation and data-compatibility features to streamline lab workflows, improve data integrity, and prepare for 2025 data processing. Focused on automated run registration, plasma/LIMS data conversion enhancements, and 2024-data readiness with robust parsing and safeguards.
December 2024
6 Commits • 3 Features
Dec 1, 20242024-12 monthly summary for hartwigmedical/scripts: Delivered automation and data-compatibility features to streamline lab workflows, improve data integrity, and prepare for 2025 data processing. Focused on automated run registration, plasma/LIMS data conversion enhancements, and 2024-data readiness with robust parsing and safeguards.
November 2024
8 Commits • 2 Features
Nov 1, 2024Monthly summary for 2024-11 (hartwigmedical/scripts). This period focused on improving data pipeline reliability and output quality through Aria tooling enhancements, robust ID handling, per-file signed URL generation, and data/holidays updates for 2024–2025. Delivered a set of targeted improvements with measurable business value by standardizing file naming, ensuring correct reporting IDs, and preventing runtime errors in ops-vm. Implemented tests for 2025 data to guard against regressions and kept the holidays calendar up to date for accurate processing timelines.
8 Commits • 2 Features
Nov 1, 2024Monthly summary for 2024-11 (hartwigmedical/scripts). This period focused on improving data pipeline reliability and output quality through Aria tooling enhancements, robust ID handling, per-file signed URL generation, and data/holidays updates for 2024–2025. Delivered a set of targeted improvements with measurable business value by standardizing file naming, ensuring correct reporting IDs, and preventing runtime errors in ops-vm. Implemented tests for 2025 data to guard against regressions and kept the holidays calendar up to date for accurate processing timelines.
November 2024
Activity
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Quality Metrics
Correctness85.0%
Maintainability86.0%
Architecture78.8%
Performance81.8%
AI Usage20.0%
Skills & Technologies
Programming Languages
BashJSONPerlPythonRR MarkdownShellbashjq
Technical Skills
API IntegrationBioinformaticsBioinformatics ScriptingBug FixingCloud InfrastructureCloud Services (GCP)Cloud StorageCloud Storage ManagementData AnalysisData CollectionData ConversionData ProcessingData TransformationData VisualizationDebugging
Repositories Contributed To
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