Snakemake-Workflows
Snakemake-Workflows
dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
docs
Documentation of the Snakemake-Workflows project
cookiecutter-snakemake-workflow
A cookiecutter template for Snakemake workflows
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 Var...
rna-seq-kallisto-sleuth
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
single-cell-rna-seq
A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
ngs-test-data
A workflow for creating small NGS test data sets, useful for continuous integration.
snakemake-workflow-template
A template for standard compliant snakemake-workflows