Genome Sequence Informatics

shesmu

Decision-driven action launching system

djerba

Create cancer bioinformatics reports from metadata and workflow output

variantEffectPredictor

Variant Effect Predictor Workflow

bamQC

Workflow to run bam-qc-metrics (https://github.com/oicr-gsi/bam-qc-metrics)

dimsum

QC Tracking dashboard

gsi-wdl-tools

pinery

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

vidarr

Analysis provenance tracking server

data_release

Scripts for releasing data generated at OICR to stakeholders

analysisProcedures

bcl2fastq

Workflow for Illumina's bcl2fastq

bclconvert

Workflow to process a run directory through Dragen bclconvert

bwamem2

workflow for bwa-men2

cardea

Case data API

cerberus

File provenance library

crosscheckFingerprints

dellyGermline

Call germline SVs using Delly

Dragen-bclconvert

empty

Empty workflow for testing infrastructure

mavis3

MAVIS workflow, annotation of structural variants

mutect2Consensus

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.

mutect2ConsensusTumorOnly

The Mutect2Consensus workflow with only tumor inputs

nabu

QC tracking for files via a web service

provenanceReporter

smallBamQc

Generate BAM file metrics for OICR's QC Gates as fast as possible

star

Workflow for STAR RNAseq aligner

t1k

variantMerging

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

vidarr-tools

The home of Python tools for use with Víðarr

xenoclassify-workflow

workflow to classify short-read sequencing data generated from xenograft samples