Patrik Smeds's repositories
ansible-bender
ansible-playbook + buildah = a sweet container image
arteria-bcl2fastq
Provides a simple http-interface for Illumina bcl2fastq
arteria-packs
StackStorm packs to automate sequencing center operations
bioconda-recipes
Conda recipes for the bioconda channel.
biocontainers
Bioinformatics containers
dna-seq-varlociraptor
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
docker-backupninja
Dockerfile for Backupninja
docker-backupninja-1
A backupninja container for handling backups.
galaxy
Data intensive science for everyone.
gms_somatic
Placeholder for solid tumor bioinformatic workflow
multiqc_cgs
MultiQC plugin that will make it possible to add more columns to general statistics table
MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
pgx
Pharmacogenomics pipeline
pgx_module
Anlysis of pharmacogenomic targets from Genomic Medicine Swedens heamatology panel.
rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
snakemake
This is the development home of the workflow management system Snakemake. For general information, see
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
st2-docker
StackStorm docker-compose deployment
tools
Python package with helper tools for the nf-core community.
wgs_std_viper
Simple workflow to map WGS data to reference genome according to GATK best practices
WorkflowSandbox
WorkflowSandbox