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nf-configs/docs/binac.md
Alexander Peltzer c2fa8d5441 Add BINAC documentation
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nf-core/configs: BINAC Configuration

All nf-core pipelines have been successfully configured for use on the BINAC cluster at the insert institution here.

To use, run the pipeline with -profile binac. This will download and launch the binac.config which has been pre-configured with a setup suitable for the BINAC cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline.

Below are non-mandatory information e.g. on modules to load etc.

Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on BINAC cluster. You can do this by issuing the commands below:

## Load Nextflow and Singularity environment modules
module purge
module load devel/java_jdk/1.8.0u112
module load devel/singularity/3.0.1

## Example command for nf-core/atacseq
nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk

All of the intermediate files required to run the pipeline will be stored in the work/ directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the results/ directory anyway.

NB: You will need an account to use the HPC cluster BINAC in order to run the pipeline. If in doubt contact IT.

NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.