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.
- Snakemake (https://bitbucket.org/johanneskoester/snakemake/overview)
- bwa (http://bio-bwa.sourceforge.net/bwa.shtml)
- samtools (http://samtools.sourceforge.net/)
- genomeCoverageBed (http://code.google.com/p/bedtools/)
- Picard (http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page)
- Change the path to the location of
sbatch_jobinSnakefile-sbatch.py - Change the location of Picard tools in
Snakefile. - Set the proper parameters in the schedule() method for your sbatch account and partition names
# 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