diff --git a/docs/nextflow.md b/docs/nextflow.md index fef9e17..e827fb3 100644 --- a/docs/nextflow.md +++ b/docs/nextflow.md @@ -9,10 +9,10 @@ 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 with `-r`: +You can specify a specific version, tag, or branch on [GitHub](https://github.com/CCBR/CHAMPAGNE) with `-r`: ```sh -nextflow run CCBR/CHAMPAGNE -r v1.0.0 -profile test,singularity +nextflow run CCBR/CHAMPAGNE -r v0.3.0 -profile test,singularity ``` Create and use a custom reference genome: @@ -21,3 +21,15 @@ 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: + +```sh +module load ccbrpipeliner +module load nextflow +nextflow run CCBR/CHAMPAGNE -profile test,biowulf,slurm +```