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nf-core/configs: CRA HPC Configuration

nfcore pipeline sarek and rnaseq have been tested on the CRA HPC.

Before running the pipeline

  • You will need an account to use the CRA HPC cluster in order to run the pipeline.
  • Make sure that Singularity and Nextflow are installed.
  • Downlode pipeline singularity images to a HPC system using nf-core tools
$ conda install nf-core
$ nf-core download
  • You will need to specify a Singularity cache directory in your ~./bashrc. This will store your container images in this cache directory without repeatedly downloading them every time you run a pipeline. Since space on home directory is limited, using lustre file system is recommended.
export NXF_SINGULARITY_CACHEDIR = "/lustre/fs0/storage/yourCRAAccount/cache_dir"
  • Download iGenome reference to be used as a local copy.
$ aws s3 --no-sign-request --region eu-west-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/ /lustre/fs0/storage/yourCRAAccount/references/Homo_sapiens/GATK/GRCh38/

Running the pipeline using the adcra config profile

  • Run the pipeline within a screen or tmux session.
  • Specify the config profile with -profile adcra.
  • Using lustre file systems to store results (--outdir) and intermediate files (-work-dir) is recommended.
nextflow run /path/to/nf-core/<pipeline-name> -profile adcra \
--genome GRCh38 \
--igenomes_base /path/to/genome_references/ \
... # the rest of pipeline flags