You cannot select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.

1.6 KiB

Raw Permalink Blame History

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