Genome Sequence Informatics

emSeqQc

Runs bwa-meth followed by bamqc and methyldackel

estimate

ESTIMATE provides researchers with scores for tumor purity, the level of stromal cells present, and the infiltration level of immune cells in tumor tissues based on expression data

hrDetect

Workflow for the sigtools and HRdetect R packages

sample-fingerprinting

workflow that generates genotype fingerprints consumed by SampleFingerprinting workflow

bcl2barcode

calculateContamination

A WDL workflow that runs GATK4 CalculateContamination from FastQ files.

consensusCruncherWorkflow

A workflow which combines consensus cruncher and mutect2

dellyGermline

Call germline SVs using Delly

dragmap

A workflow to run Dragmap

gatk-genotype-GVCFs

Genotype GVCFs WDL workflow for GATK4

hotspotFingerprintCollector

common Fingerprint Collector workflow, that aligns sequence and runs 1 or more sample fingerprinting tools

mavis

MAVIS workflow, annotation of structural variants

mavis3

MAVIS workflow, annotation of structural variants

minimap2

Workflow to align long read fastq files to a reference genome

msisensor

msisensor-pro workflow

nanoporeCoverageAnalysis

Workflow for nanopore coverage analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

nanoporeFilterFastq

Workflow for filter nanopore fastq file, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

nanoporeMapping

Workflow for nanopore reads mapping, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

nanoporeRunSVAnalysis

Workflow for running structural variants analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

nanoporeSVAll

Workflow for executing all task of nanopore filterfastq, nanopore mapping, nanopore coverage analysis, nanopore structural variants analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

ncov2019ArticNf

ncov2019ArticNf workflow executes the ncov2019-artic-nf Nextflow workflow from connor-lab (https://github.com/connor-lab/ncov2019-artic-nf).

probeCoverageDistribution

Workflow to calculate probe coverage, calls bwaMem

rsem

WDL workflow for RSEM tool (transcription analysis for RNAseq)

smallBamQc

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

sniffles

Workflow to run Structural Variant caller for Nanopore

star

Workflow for STAR RNAseq aligner

t1k

tmbAnalysis

A workflow to align fastq reads, call variants, annotate and assess TMB

umiCollapse

umiCollapse workflow, generating umi deduplicated bam file and stats

variantMerging

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