Genome Sequence Informatics's repositories
barcodex-rs
Reimplementation of barcodex for performance
ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
determinePhiX
Workflow to determine PhiX contamination of undetermined reads
Analysis_Reports
for generation of analysis reports to accompany released data
anonymize_report
A script to anonymize release reports
cbioportal_tools
tools for import of data and administration of the gsi cbioportal instance
CGI_validation_scripts
scripts for clinical validation of new assays
CHORD
A WDL implementation of UMCUGenetics CHORD
empty
Empty workflow for testing infrastructure
epif-gravity
Building software off gravity forms to pull back information about electronic project information forms
hotspotFingerprintCollector
common Fingerprint Collector workflow, that aligns sequence and runs 1 or more sample fingerprinting tools
immunedeconvWorkflow
Workflow to run immunedeconv functions
indelValidate
workflow for indel validation, based on CGI-Tools/6-indelValidate.sh
nanopore-SV-analysis
Structural variant filtering and anlaysis of Nanopore human WGS data.
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.
probeCoverageDistribution
Workflow to calculate probe coverage, calls bwaMem
ricoWorkflow
WDL workflow to run the RICO Singularity container
SEXCMD
A fork of SEXCMD repository
strelka
Workflow to run Strelka1 for variant calling
umiQC
QC workflow to assess UMI components
virusbreakend
OICR Genomics WDL for VIRUSBreakend
virusdetection
OICR Genomics kraken2 WDL workflow
wdlviz
Python tool to create DOT diagrams for WDL workflows