hartwigmedical/scripts
Nov 2024 – May 2026
16 Months active
Languages Used
BashShellPythonSQLbashAwkRAWK
Technical Skills
DevOpsScriptingShell ScriptingAPI IntegrationAPI InteractionAPI integration
Iris Stuiver
PROFILE
Iris Stuiver
Over 16 months, contributed to the hartwigmedical/scripts repository by building and refining automation, reporting, and data processing workflows for genomics and bioinformatics pipelines. Leveraging Python, Bash, and R, delivered features such as robust VCF merging, scalable bulk reporting, and secure cloud storage integration with Google Cloud Storage. Enhanced pipeline reliability through improved error handling, data validation, and configurable execution paths, while reducing manual intervention with automation scripts and API-driven tooling. Addressed bugs affecting artifact generation, reporting accuracy, and cloud file handling, resulting in more maintainable, auditable, and efficient workflows that support cross-repository data sharing and high-quality clinical reporting.
Overall Statistics
Feature vs Bugs
72%Features
Repository Contributions
99Total
Bugs
11
Commits
99
Features
28
Lines of code
4,309
Activity Months16
Your Network
66 peopleSame Organization
@hartwigmedicalfoundation.nl34
Shared Repositories
32
Work History
May 2026
1 Commits • 1 Features
May 1, 2026Monthly work summary for May 2026 focusing on feature delivery and robustness improvements in hartwigmedical/scripts. Delivered a Report Generation Enhancement to correctly handle multiple hospital names and patient cohorts, enabling accurate cross-hospital data sharing. Implemented validation and conditional logic enhancements to improve data quality and governance. The change is tracked with commit d820a63c837abd6156fd9e439902fb0fbd658225 (Add extra info and conditions to check script).
1 Commits • 1 Features
May 1, 2026Monthly work summary for May 2026 focusing on feature delivery and robustness improvements in hartwigmedical/scripts. Delivered a Report Generation Enhancement to correctly handle multiple hospital names and patient cohorts, enabling accurate cross-hospital data sharing. Implemented validation and conditional logic enhancements to improve data quality and governance. The change is tracked with commit d820a63c837abd6156fd9e439902fb0fbd658225 (Add extra info and conditions to check script).
May 2026
April 2026
5 Commits • 1 Features
Apr 1, 2026April 2026 – Hartwig Medical Scripts: Delivered scalable, reliable batch reporting enhancements and tightened data handling to improve business value and system stability.
April 2026
5 Commits • 1 Features
Apr 1, 2026April 2026 – Hartwig Medical Scripts: Delivered scalable, reliable batch reporting enhancements and tightened data handling to improve business value and system stability.
March 2026
5 Commits • 3 Features
Mar 1, 2026March 2026: Delivered three automation features across hartwigmedical/scripts, strengthening data accuracy, API-driven mapping, and bulk data sharing, while tightening the reporting pipeline with blacklist-based filtering and clearer error messaging. Highlights include: (1) reporting pipeline improvements with blacklist filtering and improved error messaging for unknown process types; (2) a new specimen ID to patient ID mapping script with API integration and robust HTTP error handling; (3) a bulk share panel data script with input validation prior to cloud upload. These workstreams reduced manual troubleshooting, improved data quality, and accelerated downstream analytics. Technologies demonstrated include Bash scripting, REST API integration, error handling, temporary/file management, and cloud storage workflows.
5 Commits • 3 Features
Mar 1, 2026March 2026: Delivered three automation features across hartwigmedical/scripts, strengthening data accuracy, API-driven mapping, and bulk data sharing, while tightening the reporting pipeline with blacklist-based filtering and clearer error messaging. Highlights include: (1) reporting pipeline improvements with blacklist filtering and improved error messaging for unknown process types; (2) a new specimen ID to patient ID mapping script with API integration and robust HTTP error handling; (3) a bulk share panel data script with input validation prior to cloud upload. These workstreams reduced manual troubleshooting, improved data quality, and accelerated downstream analytics. Technologies demonstrated include Bash scripting, REST API integration, error handling, temporary/file management, and cloud storage workflows.
March 2026
December 2025
16 Commits • 1 Features
Dec 1, 2025December 2025 monthly summary for hartwigmedical/scripts: Key features delivered: - Reporting pipeline robustness and optimization: robust data retrieval from lama and patient-reporter data, pattern-based GCS file access, improved handling of spaces in filenames, and upload optimizations to Nextcloud including only the latest patient reports; added the capability to disable the reporting pipeline in status checks. Major bugs fixed: - Suppressed report content for failed runs to reduce noise and improve result clarity. - Fixed file paths and sharing for panel reports and patient-reporter.json: corrected bucket paths and file-name patterns for reliable access via GCS and StatusChecker. Overall impact and accomplishments: - Increased reliability and efficiency of the reporting pipeline, improved data sharing and access, and safer operation via status-based disablement. Delivered changes reduce operational noise and enable faster, more trustworthy reporting. Technologies/skills demonstrated: - Google Cloud Storage patterns, Nextcloud integration, status checks controls, robust file/path handling, error resilience, and maintainable code changes.
December 2025
16 Commits • 1 Features
Dec 1, 2025December 2025 monthly summary for hartwigmedical/scripts: Key features delivered: - Reporting pipeline robustness and optimization: robust data retrieval from lama and patient-reporter data, pattern-based GCS file access, improved handling of spaces in filenames, and upload optimizations to Nextcloud including only the latest patient reports; added the capability to disable the reporting pipeline in status checks. Major bugs fixed: - Suppressed report content for failed runs to reduce noise and improve result clarity. - Fixed file paths and sharing for panel reports and patient-reporter.json: corrected bucket paths and file-name patterns for reliable access via GCS and StatusChecker. Overall impact and accomplishments: - Increased reliability and efficiency of the reporting pipeline, improved data sharing and access, and safer operation via status-based disablement. Delivered changes reduce operational noise and enable faster, more trustworthy reporting. Technologies/skills demonstrated: - Google Cloud Storage patterns, Nextcloud integration, status checks controls, robust file/path handling, error resilience, and maintainable code changes.
November 2025
12 Commits • 4 Features
Nov 1, 2025Delivered significant improvements to the Hartwig scripts pipeline in 2025-11, focusing on visibility, reliability, and cloud-enabled data processing. Implemented a new Waiting Runs Reporting chapter in the Reporting Pipeline, refined processing run summaries, enhanced germline variant handling, and added signed URL support for CRAM files in Google Cloud Storage. The work emphasizes faster issue detection, robust data processing, and secure access patterns for downstream consumers.
12 Commits • 4 Features
Nov 1, 2025Delivered significant improvements to the Hartwig scripts pipeline in 2025-11, focusing on visibility, reliability, and cloud-enabled data processing. Implemented a new Waiting Runs Reporting chapter in the Reporting Pipeline, refined processing run summaries, enhanced germline variant handling, and added signed URL support for CRAM files in Google Cloud Storage. The work emphasizes faster issue detection, robust data processing, and secure access patterns for downstream consumers.
November 2025
October 2025
8 Commits • 2 Features
Oct 1, 2025October 2025: Delivered robust data integrity and reliability improvements in hartwigmedical/scripts. Key features include: (1) enhanced report status checks with validation for reportingId presence across checks, verification that Lama data exists before further checks, logging warnings when data is missing, a syntax fix in the status script, and early returns when Lama data is not found; (2) standardized tumor genotype handling in VCF processing by defaulting missing './.' to '0/1' and ensuring precise replacement in id_snpcaller VCF. Major bug fix: corrected the serve database load path by updating the JAR location to point at the correct executable, ensuring reliable DB loading. Overall impact: improved data quality and reliability, faster diagnostics due to targeted logging, and more dependable DB loading. Technologies/skills demonstrated include Python/Bash scripting, data validation, robust logging, VCF genotype processing, and build/deploy hygiene.
October 2025
8 Commits • 2 Features
Oct 1, 2025October 2025: Delivered robust data integrity and reliability improvements in hartwigmedical/scripts. Key features include: (1) enhanced report status checks with validation for reportingId presence across checks, verification that Lama data exists before further checks, logging warnings when data is missing, a syntax fix in the status script, and early returns when Lama data is not found; (2) standardized tumor genotype handling in VCF processing by defaulting missing './.' to '0/1' and ensuring precise replacement in id_snpcaller VCF. Major bug fix: corrected the serve database load path by updating the JAR location to point at the correct executable, ensuring reliable DB loading. Overall impact: improved data quality and reliability, faster diagnostics due to targeted logging, and more dependable DB loading. Technologies/skills demonstrated include Python/Bash scripting, data validation, robust logging, VCF genotype processing, and build/deploy hygiene.
September 2025
9 Commits • 3 Features
Sep 1, 2025September 2025 monthly summary for hartwigmedical/scripts: Delivered reliability and quality improvements across the reporting pipeline, germline variant analysis, and VCF handling, with clear usability and maintenance gains. The work reduced downstream errors, improved data integrity in shared reports, and strengthened pipeline robustness for stakeholder-facing outputs.
9 Commits • 3 Features
Sep 1, 2025September 2025 monthly summary for hartwigmedical/scripts: Delivered reliability and quality improvements across the reporting pipeline, germline variant analysis, and VCF handling, with clear usability and maintenance gains. The work reduced downstream errors, improved data integrity in shared reports, and strengthened pipeline robustness for stakeholder-facing outputs.
September 2025
July 2025
1 Commits
Jul 1, 2025July 2025 monthly summary focusing on bug fix in hartwigmedical/scripts to ensure correct diagnostic context when fetching run data via API; resolved a merge conflict with master and improved reliability of run data queries. The work enhances data accuracy for downstream analytics and reduces risk of incorrect API context usage.
July 2025
1 Commits
Jul 1, 2025July 2025 monthly summary focusing on bug fix in hartwigmedical/scripts to ensure correct diagnostic context when fetching run data via API; resolved a merge conflict with master and improved reliability of run data queries. The work enhances data accuracy for downstream analytics and reduces risk of incorrect API context usage.
June 2025
15 Commits • 2 Features
Jun 1, 2025June 2025: Substantial enhancements in hartwigmedical/scripts focusing on VCF merging/sharing, pipeline configurability, and robust data handling. These changes streamline cross-workflow data integration (somatic, germline, and snpcaller), improve portal sharing readiness, and increase pipeline reliability with configurable outputs and better logging. The work delivers measurable business value by reducing manual remediation, enabling flexible deployments, and decreasing run-time failures when diagnostic data is sparse.
15 Commits • 2 Features
Jun 1, 2025June 2025: Substantial enhancements in hartwigmedical/scripts focusing on VCF merging/sharing, pipeline configurability, and robust data handling. These changes streamline cross-workflow data integration (somatic, germline, and snpcaller), improve portal sharing readiness, and increase pipeline reliability with configurable outputs and better logging. The work delivers measurable business value by reducing manual remediation, enabling flexible deployments, and decreasing run-time failures when diagnostic data is sparse.
June 2025
May 2025
5 Commits • 1 Features
May 1, 2025In May 2025, the team delivered stability and reliability improvements to the artifact generation and QC reporting pipeline in hartwigmedical/scripts. Key changes include corrections to germline gene processing references and the genenames.pass.pon.csv path to ensure accurate artifact generation/reporting; removal of legacy bamMetrics handling and related artifacts to streamline the codebase; and enforcement of PASS filters on somatic VCF variants for QC reporting to improve reliability. These changes reduce maintenance burden, minimize downstream errors, and increase trust in automated reports. Technologies demonstrated include robust R scripting (createSampleQcReport.R), data validation, and version-controlled pipelines with clear traceability of fixes and commits.
May 2025
5 Commits • 1 Features
May 1, 2025In May 2025, the team delivered stability and reliability improvements to the artifact generation and QC reporting pipeline in hartwigmedical/scripts. Key changes include corrections to germline gene processing references and the genenames.pass.pon.csv path to ensure accurate artifact generation/reporting; removal of legacy bamMetrics handling and related artifacts to streamline the codebase; and enforcement of PASS filters on somatic VCF variants for QC reporting to improve reliability. These changes reduce maintenance burden, minimize downstream errors, and increase trust in automated reports. Technologies demonstrated include robust R scripting (createSampleQcReport.R), data validation, and version-controlled pipelines with clear traceability of fixes and commits.
April 2025
1 Commits • 1 Features
Apr 1, 2025April 2025 monthly summary for hartwigmedical/scripts: Delivered a targeted enhancement to the Resource Pull Script to enable pulling from the reporting-resources repository, unifying cross-repo resource management and improving automation. No major bug fixes reported this month. Overall impact: faster provisioning, reduced manual steps, and more scalable resource management across repositories. Technologies/skills demonstrated: scripting/automation, repository automation, version-control practices, and cross-repo resource management.
1 Commits • 1 Features
Apr 1, 2025April 2025 monthly summary for hartwigmedical/scripts: Delivered a targeted enhancement to the Resource Pull Script to enable pulling from the reporting-resources repository, unifying cross-repo resource management and improving automation. No major bug fixes reported this month. Overall impact: faster provisioning, reduced manual steps, and more scalable resource management across repositories. Technologies/skills demonstrated: scripting/automation, repository automation, version-control practices, and cross-repo resource management.
April 2025
March 2025
2 Commits • 2 Features
Mar 1, 2025March 2025 performance summary for hartwigmedical/scripts focused on hardening the data sharing and reporting pipeline to improve data integrity, observability, and operational efficiency. Implemented validation to prevent partial data sharing and enhanced error visibility to speed triage, delivering measurable business value with safer data workflows and clearer incident signals.
March 2025
2 Commits • 2 Features
Mar 1, 2025March 2025 performance summary for hartwigmedical/scripts focused on hardening the data sharing and reporting pipeline to improve data integrity, observability, and operational efficiency. Implemented validation to prevent partial data sharing and enhanced error visibility to speed triage, delivering measurable business value with safer data workflows and clearer incident signals.
February 2025
5 Commits • 2 Features
Feb 1, 2025February 2025 monthly summary for hartwigmedical/scripts focusing on key features delivered, major bugs fixed, overall impact, and technologies demonstrated. Highlights include enhancements to Shared sample data upload script (3-day timestamp filtering, target filtering, improved logging, temporary file cleanup) and Serve-diff repo tooling integration (new pull_servediff_repo script, expanded pull_source_repo to include serve-diff, updated warning messaging). These changes improve data ingestion reliability, cross-repo collaboration, and observability; business value includes scalable data sharing, reduced manual intervention, and broader tooling coverage. Key commits: d539211830fdfbdde62c72f622be49312e8565e7; 372a23218341514a20af5f2c55dd22d8c4d651e3; 3e6db13e76c351af3399933d9ae3bd64c815d984; f9cebb4733a5f40f0be95f35b425e032d2d88a79; faa3114692066b461780d54d455b0a91c0687569.
5 Commits • 2 Features
Feb 1, 2025February 2025 monthly summary for hartwigmedical/scripts focusing on key features delivered, major bugs fixed, overall impact, and technologies demonstrated. Highlights include enhancements to Shared sample data upload script (3-day timestamp filtering, target filtering, improved logging, temporary file cleanup) and Serve-diff repo tooling integration (new pull_servediff_repo script, expanded pull_source_repo to include serve-diff, updated warning messaging). These changes improve data ingestion reliability, cross-repo collaboration, and observability; business value includes scalable data sharing, reduced manual intervention, and broader tooling coverage. Key commits: d539211830fdfbdde62c72f622be49312e8565e7; 372a23218341514a20af5f2c55dd22d8c4d651e3; 3e6db13e76c351af3399933d9ae3bd64c815d984; f9cebb4733a5f40f0be95f35b425e032d2d88a79; faa3114692066b461780d54d455b0a91c0687569.
February 2025
January 2025
11 Commits • 4 Features
Jan 1, 2025January 2025 monthly summary for hartwigmedical/scripts focusing on deliveringValue, reliability, and maintainability in production reporting and diagnostic tooling.
January 2025
11 Commits • 4 Features
Jan 1, 2025January 2025 monthly summary for hartwigmedical/scripts focusing on deliveringValue, reliability, and maintainability in production reporting and diagnostic tooling.
December 2024
1 Commits
Dec 1, 2024December 2024 monthly summary for hartwigmedical/scripts: Delivered a critical bug fix to IGV configuration URL handling, improving environment reliability and reducing configuration failures. The fix switches URL generation to per-file requests, updates parsing to extract the correct URL per file, and resolves has_attr-related errors on operational VMs. Result: more robust IGV integration, fewer manual workarounds, and smoother CI/CD workflows.
1 Commits
Dec 1, 2024December 2024 monthly summary for hartwigmedical/scripts: Delivered a critical bug fix to IGV configuration URL handling, improving environment reliability and reducing configuration failures. The fix switches URL generation to per-file requests, updates parsing to extract the correct URL per file, and resolves has_attr-related errors on operational VMs. Result: more robust IGV integration, fewer manual workarounds, and smoother CI/CD workflows.
December 2024
November 2024
2 Commits • 1 Features
Nov 1, 2024Month 2024-11: Focused on delivering automation for the CKB importer to improve reliability, repeatability, and data freshness. Major bugs fixed: none reported. Overall impact: automated, date-aware importer workflow that reduces manual steps and enables faster, reproducible data ingestion. Technologies/skills demonstrated: shell scripting, environment configuration, version-controlled automation, and clear commit traceability.
November 2024
2 Commits • 1 Features
Nov 1, 2024Month 2024-11: Focused on delivering automation for the CKB importer to improve reliability, repeatability, and data freshness. Major bugs fixed: none reported. Overall impact: automated, date-aware importer workflow that reduces manual steps and enables faster, reproducible data ingestion. Technologies/skills demonstrated: shell scripting, environment configuration, version-controlled automation, and clear commit traceability.
Activity
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Quality Metrics
Correctness88.4%
Maintainability86.6%
Architecture81.4%
Performance83.4%
AI Usage20.8%
Skills & Technologies
Programming Languages
AWKAwkBashGawkPythonRSQLShellawkbash
Technical Skills
API IntegrationAPI InteractionAPI integrationBackend DevelopmentBioinformaticsCloud Computing (GCS)Cloud StorageCloud Storage InteractionCloud Storage ManagementCode RefactoringData AnalysisData FilteringData ProcessingData ValidationData processing
Repositories Contributed To
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