latchbio / latch-snakemake-examples

Example Snakemake Projects

Intended to test Snakemake support on latch and provide examples for co-development.

pip install 'latch[snakemake]'

Documentation

fgbio

A set of tools to analyze genomic data developed by Fulcrum Genomics.

cd fgbio && latch register . --snakefile FastqToConsensus-RnD.smk

sv-callers

Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases. sv-callers is a Snakemake-based workflow that combines several state-of-the-art tools for detecting SVs in whole genome sequencing (WGS) data. The workflow is developed and maintained by Netherlands eScience Center project: Googling the cancer genome.

Clone the repository:

git clone https://github.com/latchbio/snakemake-sv-callers.git

Register the workflow with the Latch SDK:

cd snakemake-sv-callers && latch register . --snakefile workflow/Snakefile

kraken2_classification

A Snakemake pipeline wrapper of the Kraken2 short read metagenomic classification software, with additional tools for analysis, plots, compositional data and differential abundance calculation. Designed and maintained by Ben Siranosian in Ami Bhatt's lab at Stanford University.

Clone the repository:

git clone https://github.com/latchbio/snakemake_kraken2_classification.git

Register the workflow with the Latch SDK:

cd snakemake_kraken2_classification && latch register . --snakefile Snakefile