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87 lines
4.1 KiB
Markdown
87 lines
4.1 KiB
Markdown
# nf-core/configs: UPPMAX Configuration
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All nf-core pipelines have been successfully configured for use on the Swedish UPPMAX clusters.
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## Getting help
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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)
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## Using the UPPMAX config profile
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To use, run the pipeline with `-profile uppmax` (one hyphen).
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This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers.
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Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
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In addition to this config profile, you will also need to specify an UPPMAX project id.
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You can do this with the `--project` flag (two hyphens) when launching nextflow. For example:
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```bash
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nextflow run nf-core/PIPELINE -profile uppmax --project snic2018-1-234 # ..rest of pipeline flags
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```
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> NB: If you're not sure what your UPPMAX project ID is, try running `groups` or checking SUPR.
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Before running the pipeline you will need to either install Nextflow or load it using the environment module system.
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This config enables Nextflow to manage the pipeline jobs via the Slurm job scheduler and using Singularity for software management.
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Just run Nextflow on a login node and it will handle everything else.
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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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## Using iGenomes references
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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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You can do this by simply using the `--genome <GENOME_ID>` parameter.
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## Getting more memory
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If your nf-core pipeline run is running out of memory, you can run on a fat node with more memory using the following nextflow flags:
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```bash
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--clusterOptions "-C mem256GB" --max_memory "256GB"
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```
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This raises the ceiling of available memory from the default of `128.GB` to `256.GB`.
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Rackham has nodes with 128GB, 256GB and 1TB memory available.
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Note that each job will still start with the same request as normal, but restarted attempts with larger requests will be able to request greater amounts of memory.
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All jobs will be submitted to fat nodes using this method, so it's only for use in extreme circumstances.
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## Different UPPMAX clusters
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The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits:
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* `bianca`
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* cpus available: 16 cpus
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* memory available: 109 GB
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* `irma`
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* cpus available: 16 cpus
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* memory available: 250 GB
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* `rackham`
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* cpus available: 20 cpus
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* memory available: 125 GB
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## Development config
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If doing pipeline development work on UPPMAX, the `devel` profile allows for faster testing.
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Applied after main UPPMAX config, it overwrites certain parts of the config and submits jobs to the `devcore` queue, which has much faster queue times.
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All jobs are limited to 1 hour to be eligible for this queue and only one job allowed at a time.
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It is not suitable for use with real data.
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To use it, submit with `-profile uppmax,devel`.
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## Running on Bianca
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For security reasons, there is no internet access on Bianca so you can't download from or upload files to the cluster directly. Before running a nf-core pipeline on Bianca you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the wharf area to your Bianca project.
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You can follow the guide for downloading pipelines [for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use). Note that you will have to download the singularity images as well.
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Next transfer the pipeline and the singularity images to your project. Before running the pipeline you will have to indicate to nextflow where the singularity images are located by setting `NXF_SINGULARITY_CACHEDIR` :
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`export NXF_SINGULARITY_CACHEDIR=Your_Location_For_The_Singularity_directory/.`
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You should now be able to run your nf-core pipeline on bianca.
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