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Update computerome.md
Update with usage, heavily inspired by the UPPMAX docs
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@ -4,4 +4,27 @@ This is a first attempt at creating a profile for the Computerome 2.0 cluster.
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To use, run the pipeline with `-profile computerome`. This will download and launch the [`computerome.config`](../conf/computerome.config) which has been pre-configured with a setup suitable for the Computerome cluster.
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>NB: You will need an account to use the HPC cluster Computerome in order to run the pipeline. If in doubt contact IT.
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## Using the Computerome config profile
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Before running the pipeline you will need to load `Nextflow` using the environment module system (this can be done with e.g. `module load tools Nextflow/<VERSION>` where `VERSION` is e.g. `20.10`).
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To use, run the pipeline with `-profile computerome` (one hyphen).
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This will download and launch the [`computerome.config`](../conf/computerome.config) which has been pre-configured with a setup suitable for the Computerome servers.
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It will enable `Nextflow` to manage the pipeline jobs via the `Torque` job scheduler.
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Using this profile, `Singularity` image(s) containing required software(s) will be downloaded before execution of the pipeline.
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Recent version of `Nextflow` also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images. The computerome configuration uses your project's scratch folder as the cachedir if not specified.
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In addition to this config profile, you will also need to specify a Computerome project id.
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You can do this with the `--project` flag (two hyphens) when launching `Nextflow`.
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For example:
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```bash
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# Launch a nf-core pipeline with the computerome profile for the project id ab00002
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$ nextflow run nf-core/<PIPELINE> -profile computerome --project ab00002 [...]
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```
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> NB: If you're not sure what your Computerome project ID is, try running `groups`.
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Remember to use `-bg` to launch `Nextflow` in the background, so that the pipeline doesn't exit if you leave your terminal session.
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Alternatively, you can also launch `Nextflow` in a `screen` or a `tmux` session.
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