# 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.

> [!NOTE]
>
> CHAMPAGNE requires nextflow v25.10.0 or later.

```sh
nextflow run CCBR/CHAMPAGNE -profile test,singularity
```

You can specify a specific version, tag, or branch on [GitHub](https://github.com/CCBR/CHAMPAGNE) with `-r`:

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

Create and use a custom reference genome:

```sh
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/25.10
nextflow run CCBR/CHAMPAGNE -profile test,biowulf,slurm
```
