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24 lines
1.7 KiB
Markdown
24 lines
1.7 KiB
Markdown
# nf-core/configs: HKI Configuration
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All nf-core pipelines have been successfully configured for use on clusters at the [Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute](https://www.leibniz-hki.de/en).
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To use, run the pipeline with `-profile hki,<cluster>`. This will download and launch the [`hki.config`](../conf/hki.config) which contains specific profiles for each cluster. The number of parallel jobs that run is currently limited to 8.
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The currently available profiles are:
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- apate (uses singularity, cleanup set to true by default)
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- arges (uses singularity, cleanup set to true by default)
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- aither (uses singularity, cleanup set to true by default)
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- debug (sets cleanup to false for debugging purposes, use e.g. `profile hki,<cluster>,debug`)
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Note that Nextflow is not necessarily installed by default on the HKI HPC cluster(s). 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 HKI HPC clusters 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 HKI HPC clusters 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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