Clinical Genomics Lund's repositories
nextflow_rnaseqfus
Fusion genes identification pipeline
nextflow-modules
Shared nextflow modules and assets
PGxModule
PGxModule is an advanced Nextflow DSL2 workflow, designed to seamlessly integrate into your genomics pipeline. It empowers you to generate sample-specific reports with clinical guidelines, leveraging state-of-the-art variant detection in Genomic Medicine Sweden sequencing panels.
sarscov2-pipe
A boring sars-cov-2 pipeline
tomte
Rare disease RNA sequencing pipeline based on nfcore
bonsai-prp
Pipeline output Processing Program for Bonsai
Compare-VCF
Compare and visualize VCF files and rank scores
coyote_cli
command line interface for coyote
GrapeJuice
GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html
JASEN
Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
nextflow_ST_rnaseqfus
A rnaseq fussion detection assay at CMD
Pipeline-validation-tools
Set of tools for assisting verifications and validations.
pipeline_documentation
This repo generates automatic documentation for pipelines or tools by using a pipeline.yaml file and producing both HTML and MD documents. The MD document can be uploaded to a readthedocs server for online documentation. It uses the mkdocs format, with the required "docs" folder and related files in the project root folder.
qc_sentieon
Script to generate json with relevant QC-data for WGS and panels
raredisease
Call and score variants from WGS/WES of rare disease patients.
skierfe
Long read pipeline