Note: This repository has been archived and consolidated into: https://github.com/pepkit/pep-pipelines/

pep-snakemake

Example simple and bioinformatic pipelines using PEPs and Snakemake.

Simple pipeline

Here, we're counting lines using wc.

cd simple/pipelines
snakemake --cores 1

Bioinformatics pipeline

Here, we're aligning fastq files using bowtie2.

1. Install and configure required software

Install:

• Bowtie2 aligner
• refgenie Python package (manages Bowtie2 index)

Configure:

• initialize refgenie config (refgenie init -c path.yml)
• set REFGENIE environment variable to point to the initialized config
• obtain hg38/bowtie2_index asset (either refgenie build ... or refgenie pull ...)

2. Run the pipeline

cd bioinformatic/pipelines
snakemake --cores 4