Getting Started with CHAMPAGNE¶

TODO intro paragraph

Installation¶

CHAMPAGNE is installed on the Biowulf and FRCE clusters as part of the ccbrpipeliner module. If you'd like to run the pipeline in a different execution environment, take a look at how to run the nextflow pipeline directly.

Prepare a sample sheet¶

TODO

Initialize¶

Copy the configuration files to your current working directory

champagne init

Run¶

TODO preview, stub, mode=slurm

TODO required params

Run preview to view processes that will run:

champagne run -profile test -preview

Launch a stub run to view processes that will run and download containers:

champagne run -profile test,singularity -stub

Run the test dataset using the test profile:

champagne run -profile test,singularity

or explicitly specify the output directory and input:

champagne run -profile singularity --outdir results/test --input assets/samplesheet_test.csv

Custom reference genome¶

TODO different required params

Create and use a custom reference genome:

champagne run -profile test -entry MAKE_REFERENCE
champagne run -profile test -c results/test/genome/custom_genome.config