A Snakefile to parallelize bwa.
The purpose of this code is to demonstrate using snakemake (https://bitbucket.org/johanneskoester/snakemake/overview) to make pipelines and schedule each rule as a separate job with proper dependencies and sbatch. See also this issue:
https://bitbucket.org/johanneskoester/snakemake/issue/28/clustering-jobs-with-snakemake
The Snakefile aligns reads using bwa. The file is split up into a user defined number of reads. This way the alignment of each chunk of reads can be scheduled separately.
sbatch_job
in Snakefile-sbatch.py
Snakefile
.# make sure you are in the root dir of this repo
cd test
snakemake -j 99 --debug --immediate-submit --cluster './../Snakefile-sbatch.py {dependencies}' all