nf-configs/docs/pipeline/scflow/imperial.md

# nf-core/configs: Imperial scflow Specific Configuration

Extra specific configuration for the scflow pipeline

## Usage

To use, run the pipeline with `-profile imperial` or `-profile imperial_mb`.

This will download and launch the scflow specific [`imperial.config`](../../../conf/pipeline/scflow/imperial.config) which has been pre-configured with a setup suitable for the Imperial HPC cluster.

Example: `nextflow run nf-core/scflow -profile imperial`

## scflow specific configurations for Imperial

Specific configurations for Imperial have been made for scflow.

- Singularity `enabled` and `autoMounts` set to `true`
- Singularity `cacheDir` path set to an RDS location
- Singularity `runOptions` path set to bind (`-B`) RDS paths with container paths.
- Params `ctd_folder` set to an RDS location.
- Parms `ensembl_mappings` set to an RDS location.
Added institutional configs for Imperial and Imperial MEDBIO. Added institutional pipeline configs for scflow for Imperial and Imperial MEDBIO 2020-12-18 10:21:26 +00:00			`# nf-core/configs: Imperial scflow Specific Configuration`

			`Extra specific configuration for the scflow pipeline`

			`## Usage`

			To use, run the pipeline with `-profile imperial` or `-profile imperial_mb`.

			This will download and launch the scflow specific [`imperial.config`](../../../conf/pipeline/scflow/imperial.config) which has been pre-configured with a setup suitable for the Imperial HPC cluster.

			Example: `nextflow run nf-core/scflow -profile imperial`

			`## scflow specific configurations for Imperial`

			`Specific configurations for Imperial have been made for scflow.`

style: Run prettier 2022-03-17 23:33:31 +00:00			- Singularity `enabled` and `autoMounts` set to `true`
			- Singularity `cacheDir` path set to an RDS location
			- Singularity `runOptions` path set to bind (`-B`) RDS paths with container paths.
			- Params `ctd_folder` set to an RDS location.
			- Parms `ensembl_mappings` set to an RDS location.