Repositories list

• shesmu

  Public
  Decision-driven action launching system

  infrastructurebioinformaticsbioinformatics-pipeline+ 2workflow-managementworkflow-launching

  Java

  •

  MIT License

  •4•8•0•1•Updated Jan 9, 2025Jan 9, 2025

• djerba

  Public
  Create cancer bioinformatics reports from metadata and workflow output

  infrastructureinterpretation

  Python

  •

  GNU General Public License v3.0

  •4•9•5•6•Updated Jan 9, 2025Jan 9, 2025

• kallisto

  Public
  Quantifying abundances of transcripts from RNA-Seq data

  0•0•0•1•Updated Jan 8, 2025Jan 8, 2025

• cerberus

  Public
  File provenance library

  infrastructure

  Java

  •

  MIT License

  •0•0•0•0•Updated Jan 8, 2025Jan 8, 2025

• dimsum

  Public
  QC Tracking dashboard

  infrastructure

  Java

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jan 8, 2025Jan 8, 2025

• Gaea

  Public
  Register genomics data in EGA

  toolsrelease

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 7, 2025Jan 7, 2025

• gsi-wdl-tools

  Public
  toolsworkflow-dev

  Python

  •0•1•0•0•Updated Jan 3, 2025Jan 3, 2025

• vardict

  Public
  0•0•0•1•Updated Jan 3, 2025Jan 3, 2025

• smmipQC

  Public
  Set up manual smMip QC analyses

  workflow

  Python

  •0•0•0•0•Updated Dec 23, 2024Dec 23, 2024

• arriba

  Public
  Fusion caller which runs off of STAR bam

  workflow

  WDL

  •0•2•0•0•Updated Dec 20, 2024Dec 20, 2024

• mrdetect

  Public
  workflow to detect Minimal Residual disease with MRDetect

  workflow

  WDL

  •0•0•1•1•Updated Dec 19, 2024Dec 19, 2024

• vidarrTracker

  Public
  A simple logger of workflow deployment to vidarr instances

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• jira-rest-java-client

  Public
  Fork of Atlassian's JIRA REST Java Client (https://bitbucket.org/atlassian/jira-rest-java-client/)

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• cardea

  Public
  Case data API

  infrastructure

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• msisensor

  Public
  msisensor-pro workflow

  workflow

  WDL

  •0•0•0•1•Updated Dec 19, 2024Dec 19, 2024

• pinery

  Public
  A LIMS abstraction layer to provide generalized LIMS access via a web service.

  infrastructure

  Java

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Dec 16, 2024Dec 16, 2024

• nabu

  Public
  QC tracking for files via a web service

  infrastructure

  JavaScript

  •

  MIT License

  •0•0•2•0•Updated Dec 16, 2024Dec 16, 2024

• data_release

  Public
  Scripts for releasing data generated at OICR to stakeholders

  infrastructureanalysis

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

• mutect2Consensus

  Public
  The Mutect2Consensus workflow will process umiConsensus outputs for the tumour data through mutect2 in tumour only mode to call variants then use information from the matched normal to identify likely germline variants.

  workflow

  WDL

  •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• optitype

  Public
  Workflow for HLA genotyping prediction with optitype

  WDL

  •0•0•0•1•Updated Dec 11, 2024Dec 11, 2024

• vidarr

  Public
  Analysis provenance tracking server

  infrastructure

  Java

  •

  MIT License

  •1•1•0•1•Updated Dec 6, 2024Dec 6, 2024

• sampuru

  Public
  Answers the question: "where's my sample?"

  infrastructure

  Java

  •0•0•0•2•Updated Dec 6, 2024Dec 6, 2024

• crosscheck_fingerprint_caller

  Public
  To call sequencing library swaps and matches from CrosscheckFingerprints output given OICR metadata

  Python

  •0•0•0•0•Updated Nov 28, 2024Nov 28, 2024

• crosscheckFingerprintCaller

  Public
  To call sequencing library swaps and matches from CrosscheckFingerprints output given OICR metadata

  WDL

  •0•0•0•0•Updated Nov 28, 2024Nov 28, 2024

• Dragen-somatic

  Public
  The Dragen somatic variant calling workflow

  workflow

  WDL

  •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

• smmipQCReport

  Public
  Scripts to generate a summary table with QC metrics for each smMIP libraries

  toolsanalysis

  Python

  •0•0•0•0•Updated Nov 25, 2024Nov 25, 2024

• bamToFastq

  Public
  Generate R1 and R2

  workflow

  WDL

  •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• flask_ui

  Public
  projectconfig UI

  toolspipeline

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• illumina-run-dirs

  Public
  toolsdata-management

  Perl

  •

  MIT License

  •0•0•1•0•Updated Nov 19, 2024Nov 19, 2024

• biomodalQC

  Public
  QC workflow for biomodal pipeline

  WDL

  •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024