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

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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 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.