hartwigmedical/scripts
Nov 2024 – Jan 2026
13 Months active
Languages Used
PerlRShelljqbashBashJSONPython
Technical Skills
API IntegrationCloud StorageData ProcessingFile HandlingFile ManagementScripting
Yannick Bijl
PROFILE
Yannick Bijl
Over thirteen months, contributed to the hartwigmedical/scripts repository by building and refining data processing pipelines, quality control tooling, and workflow automation for genomic sequencing operations. Leveraged Python, Bash, and R to implement robust API integrations, automate sample registration, and enhance data validation and reporting. Improved pipeline reliability through memory management, error handling, and test coverage, while streamlining workflows by consolidating scripts and removing legacy dependencies. Enhanced data integrity with precise QC metrics, expanded support for new sequencing platforms, and optimized resource allocation. The work emphasized maintainability, operational efficiency, and clear data organization, supporting scalable, high-quality bioinformatics and cloud-based analytics.
Overall Statistics
Feature vs Bugs
74%Features
Repository Contributions
97Total
Bugs
11
Commits
97
Features
32
Lines of code
10,656
Activity Months13
Your Network
66 peopleSame Organization
@hartwigmedicalfoundation.nl34
Shared Repositories
32
Work History
January 2026
3 Commits • 3 Features
Jan 1, 2026January 2026: Delivered key data analysis enhancements and code quality improvements in hartwigmedical/scripts, focusing on expanding NovaSeqX coverage, refining RNA data export formats, and removing hardcoded values to boost maintainability. These changes strengthen data pipeline capabilities for NovaSeqX workflows, improve output quality, and reduce technical debt, enabling faster future feature delivery and easier maintenance across the analytics stack.
3 Commits • 3 Features
Jan 1, 2026January 2026: Delivered key data analysis enhancements and code quality improvements in hartwigmedical/scripts, focusing on expanding NovaSeqX coverage, refining RNA data export formats, and removing hardcoded values to boost maintainability. These changes strengthen data pipeline capabilities for NovaSeqX workflows, improve output quality, and reduce technical debt, enabling faster future feature delivery and easier maintenance across the analytics stack.
January 2026
December 2025
18 Commits • 5 Features
Dec 1, 2025December 2025 performance summary for hartwigmedical/scripts. Delivered data-quality enhancements, streamlined production workflows, and reliability improvements across sequencing submission pipelines, positioning the team to scale with fewer dependencies and faster turnarounds. Key work included expanding sample sheet validation for Iseq runs, enabling NovaSeqX FASTQ submission support, and consolidating production scripts into a dedicated repository, reducing maintenance overhead and risk. A critical API fix improved barcode handling by enforcing a 10-character ref_isolation_barcode, preventing unfindable barcodes. Additional improvements to NextCloud downloads and removal of obsolete scripts further reduced technical debt and improved deployment confidence. These efforts collectively improve data integrity, operational efficiency, and end-to-end submission reliability, driving business value through faster, more dependable sequencing workflows.
December 2025
18 Commits • 5 Features
Dec 1, 2025December 2025 performance summary for hartwigmedical/scripts. Delivered data-quality enhancements, streamlined production workflows, and reliability improvements across sequencing submission pipelines, positioning the team to scale with fewer dependencies and faster turnarounds. Key work included expanding sample sheet validation for Iseq runs, enabling NovaSeqX FASTQ submission support, and consolidating production scripts into a dedicated repository, reducing maintenance overhead and risk. A critical API fix improved barcode handling by enforcing a 10-character ref_isolation_barcode, preventing unfindable barcodes. Additional improvements to NextCloud downloads and removal of obsolete scripts further reduced technical debt and improved deployment confidence. These efforts collectively improve data integrity, operational efficiency, and end-to-end submission reliability, driving business value through faster, more dependable sequencing workflows.
November 2025
6 Commits • 3 Features
Nov 1, 2025November 2025 monthly summary for hartwigmedical/scripts focusing on feature delivery, quality control improvements, and workflow enhancements that drive data quality and operational clarity. The month included targeted changes to shallow QC logic, enhanced NovaSeq sample sheet processing, and cleanup of legacy registration artifacts to reduce confusion and ensure consistent data handling across the pipeline.
6 Commits • 3 Features
Nov 1, 2025November 2025 monthly summary for hartwigmedical/scripts focusing on feature delivery, quality control improvements, and workflow enhancements that drive data quality and operational clarity. The month included targeted changes to shallow QC logic, enhanced NovaSeq sample sheet processing, and cleanup of legacy registration artifacts to reduce confusion and ensure consistent data handling across the pipeline.
November 2025
October 2025
6 Commits • 1 Features
Oct 1, 2025October 2025 – Hartwig Medical's script repo delivered targeted features and reliability improvements that directly boost reporting accuracy, cross‑environment stability, and pipeline hygiene. The work emphasizes business value through clearer contact data handling, robust logging, cross‑platform script execution, and streamlined documentation and cleanup, with full commit traceability.
October 2025
6 Commits • 1 Features
Oct 1, 2025October 2025 – Hartwig Medical's script repo delivered targeted features and reliability improvements that directly boost reporting accuracy, cross‑environment stability, and pipeline hygiene. The work emphasizes business value through clearer contact data handling, robust logging, cross‑platform script execution, and streamlined documentation and cleanup, with full commit traceability.
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
Correctness88.4%
Maintainability87.8%
Architecture83.0%
Performance85.2%
AI Usage20.2%
Skills & Technologies
Programming Languages
BashJSONPerlPythonRR MarkdownShellbashjqpython
Technical Skills
API IntegrationAPI integrationBioinformaticsBioinformatics ScriptingBug FixingCloud InfrastructureCloud Services (GCP)Cloud StorageCloud Storage ManagementData AnalysisData CollectionData ConversionData ProcessingData TransformationData Visualization
Repositories Contributed To
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