nextflow pipeline¶

You can run the nextflow pipeline directly by specifying this GitHub repo. You will need nextflow and either singularity or docker installed. In this case you don't need to run champagne init first, as the config files will be accessed directly from the GitHub repo.

nextflow run CCBR/CHAMPAGNE -profile test,singularity

You can specify a specific version, tag, or branch on GitHub with -r:

nextflow run CCBR/CHAMPAGNE -r v0.3.0 -profile test,singularity

Create and use a custom reference genome:

nextflow run CCBR/CHAMPAGNE -profile test -entry MAKE_REFERENCE
nextflow run CCBR/CHAMPAGNE -profile test -c results/test/genome/custom_genome.config

biowulf¶

If you're running it on biowulf without the champagne CLI, first load the ccbrpipeliner and nextflow modules, and be sure to specify the biowulf and slurm profiles:

module load ccbrpipeliner
module load nextflow
nextflow run CCBR/CHAMPAGNE -profile test,biowulf,slurm