Repositories list

• mrdetect

  Public
  workflow to detect Minimal Residual disease with MRDetect

  workflow

  WDL

  •0•0•1•1•Updated Nov 6, 2024Nov 6, 2024

• biomodalQC

  Public
  QC workflow for biomodal pipeline

  WDL

  •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• djerba

  Public
  Create cancer bioinformatics reports from metadata and workflow output

  infrastructureinterpretation

  Python

  •

  GNU General Public License v3.0

  •4•9•4•6•Updated Nov 5, 2024Nov 5, 2024

• optitype

  Public
  Workflow for HLA genotyping prediction with optitype

  WDL

  •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• dimsum

  Public
  QC Tracking dashboard

  infrastructure

  Java

  •

  GNU General Public License v3.0

  •0•1•0•2•Updated Nov 4, 2024Nov 4, 2024

• nabu

  Public
  QC tracking for files via a web service

  infrastructure

  JavaScript

  •

  MIT License

  •0•0•2•4•Updated Nov 4, 2024Nov 4, 2024

• shesmu

  Public
  Decision-driven action launching system

  infrastructurebioinformaticsbioinformatics-pipeline+ 2workflow-managementworkflow-launching

  Java

  •

  MIT License

  •4•8•0•1•Updated Nov 4, 2024Nov 4, 2024

• cardea

  Public
  Case data API

  infrastructure

  Java

  •

  Apache License 2.0

  •0•0•0•1•Updated Nov 4, 2024Nov 4, 2024

• callability

  Public
  workflow

  WDL

  •1•0•1•2•Updated Nov 1, 2024Nov 1, 2024

• smmipQC

  Public
  Set up manual smMip QC analyses

  workflow

  Python

  •0•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• bamToFastq

  Public
  Generate R1 and R2

  workflow

  WDL

  •0•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• vidarr

  Public
  Analysis provenance tracking server

  infrastructure

  Java

  •

  MIT License

  •1•1•0•0•Updated Oct 30, 2024Oct 30, 2024

• smmipQCReport

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

  toolsanalysis

  Python

  •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

• cerberus

  Public
  File provenance library

  infrastructure

  Java

  •

  MIT License

  •0•0•0•2•Updated Oct 29, 2024Oct 29, 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 Oct 24, 2024Oct 24, 2024

• sampuru

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

  infrastructure

  Java

  •0•0•0•8•Updated Oct 19, 2024Oct 19, 2024

• data_release

  Public
  Scripts for releasing data generated at OICR to stakeholders

  infrastructureanalysis

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 18, 2024Oct 18, 2024

• dashi

  Public
  Python Dash visualization of OICR QC data

  infrastructureqc

  Python

  •

  MIT License

  •2•4•0•1•Updated Oct 18, 2024Oct 18, 2024

• bclconvert

  Public
  Workflow to process a run directory through Dragen bclconvert

  workflow

  WDL

  •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

• flask_ui

  Public
  projectconfig UI

  toolspipeline

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024

• Nextflow_WG_pipeline

  Public
  workflow

  Nextflow

  •0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

• provenanceReporter

  Public
  infrastructureanalysis

  Python

  •0•0•0•0•Updated Sep 27, 2024Sep 27, 2024

• pinery-reports

  Public
  Reports based on data from Pinery

  infrastructureqc

  Java

  •

  GNU Lesser General Public License v3.0

  •1•0•0•1•Updated Sep 25, 2024Sep 25, 2024

• illumina-run-dirs

  Public
  toolsdata-management

  Perl

  •

  MIT License

  •0•0•1•1•Updated Sep 24, 2024Sep 24, 2024

• purple

  Public
  workflow

  WDL

  •0•1•0•0•Updated Sep 12, 2024Sep 12, 2024

• wgsPipeline

  Public archive
  workflow

  0•0•0•0•Updated Aug 28, 2024Aug 28, 2024

• delly

  Public
  Delly workflow produces a set of vcf files with different types of structural variant calls

  workflowvariant-callingstructural-variation

  WDL

  •2•1•0•0•Updated Aug 27, 2024Aug 27, 2024

• variantEffectPredictor

  Public
  Variant Effect Predictor Workflow

  workflow

  WDL

  •1•3•1•1•Updated Aug 20, 2024Aug 20, 2024

• cBioPortal_Importer

  Public
  Scripts to facilitate loading data into cBioPortal

  toolsrelease

  Python

  •0•0•0•1•Updated Aug 7, 2024Aug 7, 2024

• bcl2fastq

  Public
  Workflow for Illumina's bcl2fastq

  workflowilluminabcl2fastq+ 1base-calling

  C++

  •1•0•0•1•Updated Jul 15, 2024Jul 15, 2024