clinical-genomics-lund Goto Github PK

nextflow_tumwgs

nextflow_twist-brca

Nextflow pipeline for TWIST-BRCA

nextflow_wgs

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.

pgx_module

Anlysis of pharmacogenomic targets from Genomic Medicine Swedens heamatology panel.

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

rank-model-validation-2023

raredisease

Call and score variants from WGS/WES of rare disease patients.

run_rtg

Simple script to facilitate evaluation of GIAB using RTG

sarscov2-pipe

A boring sars-cov-2 pipeline

scout

VCF visualization interface

scout-rerunner

Service for toggling re-scoring of variants with an updated pedigree

seqmon

Scripts for information monitors at CMD

skierfe

Long read pipeline

somaticpanelpipeline

tmb-calc

Calculates TMB in tumor samples from VCFs

tomte

Rare disease RNA sequencing pipeline based on nfcore

twist_dna_hematology