mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-10 20:13:09 +00:00
89 lines
4.2 KiB
Markdown
89 lines
4.2 KiB
Markdown
# nf-core/configs: UPPMAX Configuration
|
|
|
|
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
|
|
|
|
To use, run the pipeline with `-profile uppmax` (one hyphen).
|
|
This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers.
|
|
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.
|
|
|
|
In addition to this config profile, you will also need to specify an UPPMAX project id.
|
|
You can do this with the `--project` flag (two hyphens) when launching nextflow. For example:
|
|
|
|
```bash
|
|
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.
|
|
|
|
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.
|
|
|
|
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
|
|
|
|
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`.
|
|
You can do this by simply using the `--genome <GENOME_ID>` parameter.
|
|
|
|
## Getting more memory
|
|
|
|
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:
|
|
|
|
```bash
|
|
--clusterOptions "-C mem256GB" --max_memory "256GB"
|
|
```
|
|
|
|
This raises the ceiling of available memory from the default of `128.GB` to `256.GB`.
|
|
Rackham has nodes with 128GB, 256GB and 1TB memory available.
|
|
|
|
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.
|
|
|
|
All jobs will be submitted to fat nodes using this method, so it's only for use in extreme circumstances.
|
|
|
|
## Different UPPMAX clusters
|
|
|
|
The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits:
|
|
|
|
* `bianca`
|
|
* cpus available: 16 cpus
|
|
* memory available: 109 GB
|
|
* `irma`
|
|
* cpus available: 16 cpus
|
|
* memory available: 250 GB
|
|
* `rackham`
|
|
* cpus available: 20 cpus
|
|
* memory available: 125 GB
|
|
|
|
## Development config
|
|
|
|
If doing pipeline development work on UPPMAX, the `devel` profile allows for faster testing.
|
|
|
|
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.
|
|
|
|
All jobs are limited to 1 hour to be eligible for this queue and only one job allowed at a time.
|
|
It is not suitable for use with real data.
|
|
|
|
To use it, submit with `-profile uppmax,devel`.
|
|
|
|
|
|
## Running on Bianca
|
|
|
|
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.
|
|
|
|
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.
|
|
|
|
|
|
After transffering 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` :
|
|
|
|
`export NXF_SINGULARITY_CACHEDIR=Your_Location_For_The_Singularity_directory/.`
|
|
|
|
You should now be able to run your nf-core pipeline on bianca.
|