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57 lines
2.9 KiB
Markdown
57 lines
2.9 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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## Using the UPPMAX config profile
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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.
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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 SNIC 2018/1-234 # ..rest of pipeline flags
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```
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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.
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Just run Nextflow on a login node and it will handle everything else.
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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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## Running offline with Bianca
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If running on Bianca, you will have no internet connection and these configs will not be loaded.
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Please use the nf-core helper tool on a different system to download the required pipeline files, and transfer them to bianca.
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This helper tool bundles the config files in this repo together with the pipeline files, so the profile will still be available.
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Note that Bianca only allocates 7 GB memory per core so the max memory needs to be limited:
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```bash
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--max_memory "112GB"
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```
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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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## Uppmax-devel config
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If doing pipeline development work on Uppmax, this 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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