This is a port to Bpipe of the basic variant-calling and annotation pipeline developed at the Victorian Life Sciences Computation Initiative (VLSCI), University of Melbourne.
See https://github.com/claresloggett/variant_calling_pipeline/
This example is intended as an illustration of how a full pipeline looks in Bpipe, especially for those who might be familiar with Ruffus. There are a number of places where the pipeline is non-ideal, but it has been kept that way to reflect the original as accurately as possible.
One particular point of note is that the alignment output is stored in SAM format by some of the intermediate stages which would be very unadvisable for true whole-genome data. It is easy to make it store output in BAM format instead, so this would be a very advisable change if you intend to run this pipeline on a lot of data.
There are a number of software requirements, which you should ensure are satisfied before running the pipeline. These need to be configured in the file called 'config.groovy'. A template is provided in config.groovy.template which you can use to create the file and set the right paths to your tools and reference data.
By default this pipeline will attempt to use all the available cores on the computer it runs on. If you don't wish to do that, limit the concurrency by running it with the -n flag:
bpipe run -n 4 pipeline.groovy example_data/input_data_wgs/*.fastq.gz
Assumes: paired end reads Assumes: files in form <sample_name>_...R1.fastq.gz, <sample_name>..._R2.fastq.gz Assumes: Bpipe Version 0.9.8.5 or later
Note: if you just want to have a look at how the pipeline appears, you can find all the meat in the following two files:
https://github.com/ssadedin/variant_calling_pipeline/blob/master/pipeline_stages_config.groovy https://github.com/ssadedin/variant_calling_pipeline/blob/master/pipeline.groovy