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18 lines
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Markdown
18 lines
1.5 KiB
Markdown
# nf-core/configs: Cambridge HPC Configuration
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All nf-core pipelines have been successfully configured for use on the Cambridge HPC cluster at the [The University of Cambridge](https://www.cam.ac.uk/).
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To use, run the pipeline with `-profile cambridge`. This will download and launch the [`cambridge.config`](../conf/cambridge.config) which has been pre-configured
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with a setup suitable for the Cambridge HPC cluster. Using this profile, either a docker image containing all of the required software will be downloaded,
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and converted to a Singularity image or a Singularity image downloaded directly before execution of the pipeline.
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The latest version of Nextflow is not installed by default on the Cambridge HPC cluster. You will need to install it into a directory you have write access to.
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Follow these instructions from the Nextflow documentation.
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- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
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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
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has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
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> NB: You will need an account to use the Cambridge HPC cluster in order to run the pipeline. If in doubt contact IT.
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> NB: Nextflow will need to submit the jobs via SLURM to the Cambridge HPC cluster and as such the commands above will have to be executed on one of the login
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> nodes. If in doubt contact IT.
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