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Better UPPMAX docs

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Phil Ewels 2020-11-25 22:45:16 +01:00
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docs/uppmax.md
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All nf-core pipelines have been successfully configured for use on the Swedish UPPMAX clusters. All nf-core pipelines have been successfully configured for use on the Swedish UPPMAX clusters.
## Getting help
We have a Slack channel dedicated to UPPMAX users on the nf-core Slack: [https://nfcore.slack.com/channels/uppmax](https://nfcore.slack.com/channels/uppmax)
## Using the UPPMAX config profile ## Using the UPPMAX config profile
To use, run the pipeline with `-profile uppmax` (one hyphen). To use, run the pipeline with `-profile uppmax` (one hyphen).
@ -12,14 +16,19 @@ In addition to this config profile, you will also need to specify an UPPMAX proj
You can do this with the `--project` flag (two hyphens) when launching nextflow. For example: You can do this with the `--project` flag (two hyphens) when launching nextflow. For example:
```bash ```bash
nextflow run nf-core/PIPELINE -profile uppmax --project SNIC 2018/1-234 # ..rest of pipeline flags nextflow run nf-core/PIPELINE -profile uppmax --project "snic2018-1-234" # ..rest of pipeline flags
``` ```
> NB: If you're not sure what your UPPMAX project ID is, try running `groups` or checking SUPR.
Before running the pipeline you will need to either install Nextflow or load it using the environment module system. Before running the pipeline you will need to either install Nextflow or load it using the environment module system.
This config enables Nextflow to manage the pipeline jobs via the Slurm job scheduler. This config enables Nextflow to manage the pipeline jobs via the Slurm job scheduler and using Singularity for software management.
Just run Nextflow on a login node and it will handle everything else. Just run Nextflow on a login node and it will handle everything else.
Remember to use `-bg` to launch Nextflow in the background, so that the pipeline doesn't exit if you leave your terminal session.
## Using iGenomes references ## Using iGenomes references
A local copy of the iGenomes resource has been made available on all UPPMAX clusters so you should be able to run the pipeline against any reference available in the `igenomes.config`. A local copy of the iGenomes resource has been made available on all UPPMAX clusters so you should be able to run the pipeline against any reference available in the `igenomes.config`.
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All jobs will be submitted to fat nodes using this method, so it's only for use in extreme circumstances. All jobs will be submitted to fat nodes using this method, so it's only for use in extreme circumstances.
## How to specify a UPPMAX cluster ## Different UPPMAX clusters
The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits: The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits: