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Template repository

alissa_api_tools

Contain scripts to interact with Alissa API and to make VCF chunks (of a size suitable for upload to Alissa via the API)

annotate_manta_canvas

b_allele_igv_plot

balsamic_wrapper

Wrappers & tools for balsamic

canvas_to_interpreter

Converts Canvas VCF-format to format accepted by variant interpreter

cellophane

A library for creating modular wrappers.

cellophane_modules

Modules repository for cellophane

cellophane_modules_legacy

Modules to be used by cellophane wrappers

crc

fluffy_somatic_wgs

Snakemake workflow for somatic whole genome data

gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).

gms-raredisease_rna_workflow

Main repository here:

insilico_wgs

nf-core-configs

Config files used to define parameters specific to compute environments at different Institutions

nf-core-modules

Main repository here:

nf-core-raredisease

Main pipeline here:

ngpinterface

npm1_deepseq

Analysis pipeline for Ultra Deep Sequencing of NPM1

parca

Pathogen Resistance in Clinical Applications

qd-rnaseq-wrapper

This is a wrapper for starting nf-core/rnaseq and nf-core/rnafusion on a set of fastq files

qd_rna

Quick and Dirty RNA-Seq analysis pipeline

rnafusion

RNA-seq analysis pipeline for detection gene-fusions

smug

Sequencing- and Metadata Uploader for the National genomics platform (NGP)

somatic-twist

gbg fork of the uppsala pipeline being used as of summer 2022

taxprofiler-metagenomics

Taxprofiler and Parser on medstore

test-datasets

Test data to be used for automated testing with the nf-core pipelines

tomte-cgg

usage of tomte by Clinical Genomics Gothenburg

twist_dna

twist_dna_solid

Pipeline for Solid tumours