nf-configs/docs/pipeline/sarek/uppmax.md

# nf-core/configs: uppmax sarek specific configuration

Extra specific configuration for sarek pipeline

## Usage

To use, run the pipeline with `-profile uppmax`.

This will download and launch the sarek specific [`uppmax.config`](../../../conf/pipeline/sarek/uppmax.config) which has been pre-configured with a setup suitable for uppmax clusters.

Example: `nextflow run nf-core/sarek -profile uppmax`

## Sarek specific configurations for uppmax clusters

Specific configurations for uppmax clusters has been made for sarek.

- Set paths to reference genomes
- Set path to singularity containers for `irma`
add UPPMAX specific sarek config 2020-02-20 16:14:18 +00:00			`# nf-core/configs: uppmax sarek specific configuration`

			`Extra specific configuration for sarek pipeline`

			`## Usage`

			To use, run the pipeline with `-profile uppmax`.

fix path to config files 2020-03-11 13:11:23 +00:00			This will download and launch the sarek specific [`uppmax.config`](../../../conf/pipeline/sarek/uppmax.config) which has been pre-configured with a setup suitable for uppmax clusters.
add UPPMAX specific sarek config 2020-02-20 16:14:18 +00:00
			Example: `nextflow run nf-core/sarek -profile uppmax`

			`## Sarek specific configurations for uppmax clusters`

			`Specific configurations for uppmax clusters has been made for sarek.`

style: Run prettier 2022-03-17 23:33:31 +00:00			`- Set paths to reference genomes`
			- Set path to singularity containers for `irma`