Getting Started with CRISPIN¶

TODO intro paragraph

Installation¶

CRISPIN 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

crispin init

Run¶

TODO preview, stub, mode=slurm

TODO required params

Run preview to view processes that will run:

crispin run -profile test -preview

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

crispin run -profile test,singularity -stub

Run the test dataset using the test profile:

crispin run -profile test,singularity

or explicitly specify the output directory and input:

crispin 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:

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