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18 lines
1.5 KiB
Markdown
18 lines
1.5 KiB
Markdown
# nf-core/configs: SAHMRI HPC Configuration
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All nf-core pipelines have been successfully configured for use on the HPC cluster at [SAHMRI](https://sahmri.org.au/).
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To use, run the pipeline with `-profile sahmri`. This will download and launch the [`sahmri.config`](../conf/sahmri.config) which has been pre-configured
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with a setup suitable for the SAHMRI 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 SAHMRI 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 SAHMRI HPC cluster in order to run the pipeline. If in doubt contact the ICT Service Desk.
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> NB: Nextflow will need to submit the jobs via SLURM to the SAHMRI HPC cluster and as such the commands above will have to be executed on the login
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> node. If in doubt contact ICT.
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