Repositories list

• variantMerging

  Public
  a workflow for combining variant calls from SNV analyses done with different callers

  workflowutilityvariant-analysis

  Python

  •

  GNU General Public License v2.0

  •0•0•0•1•Updated Jan 28, 2025Jan 28, 2025

• dimsum

  Public
  QC Tracking dashboard

  infrastructure

  Java

  •

  GNU General Public License v3.0

  •0•1•0•4•Updated Jan 28, 2025Jan 28, 2025

• vidarrTracker

  Public
  A simple logger of workflow deployment to vidarr instances

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

• vardict

  Public
  0•0•0•1•Updated Jan 27, 2025Jan 27, 2025

• djerba

  Public
  Create cancer bioinformatics reports from metadata and workflow output

  infrastructureinterpretation

  Python

  •

  GNU General Public License v3.0

  •5•9•5•5•Updated Jan 24, 2025Jan 24, 2025

• vidarr

  Public
  Analysis provenance tracking server

  infrastructure

  Java

  •

  MIT License

  •1•1•0•1•Updated Jan 24, 2025Jan 24, 2025

• shesmu

  Public
  Decision-driven action launching system

  infrastructurebioinformaticsbioinformatics-pipeline+ 2workflow-managementworkflow-launching

  Java

  •

  MIT License

  •4•8•0•1•Updated Jan 24, 2025Jan 24, 2025

• cardea

  Public
  Case data API

  infrastructure

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• dashi

  Public
  Python Dash visualization of OICR QC data

  infrastructureqc

  Python

  •

  MIT License

  •2•4•0•1•Updated Jan 22, 2025Jan 22, 2025

• Dragen-Align

  Public
  Lane Level (single fastq pair) alignments using Dragen

  workflow

  WDL

  •0•0•0•1•Updated Jan 21, 2025Jan 21, 2025

• mrdetect

  Public
  workflow to detect Minimal Residual disease with MRDetect

  workflow

  WDL

  •0•0•1•0•Updated Jan 21, 2025Jan 21, 2025

• Dragen-germline

  Public
  workflow for running DRAGEN SNV caller in germline mode

  WDL

  •0•0•0•0•Updated Jan 20, 2025Jan 20, 2025

• Dragen-somatic

  Public
  The Dragen somatic variant calling workflow

  workflow

  WDL

  •0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

• kallisto

  Public
  Quantifying abundances of transcripts from RNA-Seq data

  WDL

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• optitype

  Public
  Workflow for HLA genotyping prediction with optitype

  WDL

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• mutect2ConsensusTumorOnly

  Public
  The Mutect2Consensus workflow with only tumor inputs

  workflow

  WDL

  •0•0•0•1•Updated Jan 13, 2025Jan 13, 2025

• Gaea

  Public
  Register genomics data in EGA

  toolsrelease

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• cerberus

  Public
  File provenance library

  infrastructure

  Java

  •

  MIT License

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

• gsi-wdl-tools

  Public
  toolsworkflow-dev

  Python

  •0•1•0•0•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

• 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

• 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

• 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