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 (eitherrefgenie build ...
orrefgenie pull ...
)
2. Run the pipeline
cd bioinformatic/pipelines
snakemake --cores 4