mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-25 17:29:55 +00:00
51 lines
2.8 KiB
Markdown
51 lines
2.8 KiB
Markdown
# nf-core/configs: UPPMAX Configuration
|
|
|
|
All nf-core pipelines have been successfully configured for use on the Swedish UPPMAX clusters.
|
|
|
|
## 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 SNIC 2018/1-234 # ..rest of pipeline flags
|
|
```
|
|
|
|
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.
|
|
Just run Nextflow on a login node and it will handle everything else.
|
|
|
|
## 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.
|
|
|
|
## Running offline with Bianca
|
|
If running on Bianca, you will have no internet connection and these configs will not be loaded.
|
|
Please use the nf-core helper tool on a different system to download the required pipeline files, and transfer them to bianca.
|
|
This helper tool bundles the config files in this repo together with the pipeline files, so the profile will still be available.
|
|
|
|
## 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.
|
|
|
|
## Uppmax-devel config
|
|
If doing pipeline development work on Uppmax, this 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`.
|