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feat: more details

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MaxUlysse 2021-04-21 11:23:50 +02:00
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docs/uppmax.md
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@ -8,18 +8,18 @@ We have a Slack channel dedicated to UPPMAX users on the nf-core Slack: [https:/
## Using the UPPMAX config profile
Before running the pipeline you will need to either install Nextflow or load it using the environment module system (this can be done with e.g. `module load bioinfo-tools Nextflow/<VERSION>` where `VERSION` is e.g. `20.10`).
Before running the pipeline you will need to either install `Nextflow` or load it using the environment module system (this can be done with e.g. `module load bioinfo-tools Nextflow/<VERSION>` where `VERSION` is e.g. `20.10`).
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.
It will enable Nextflow to manage the pipeline jobs via the Slurm job scheduler.
Using this profile, Docker image(s) containing required software(s) will be downloaded, and converted to Singularity image(s) if needed before execution of the pipeline.
It will enable `Nextflow` to manage the pipeline jobs via the `Slurm` job scheduler.
Using this profile, `Docker` image(s) containing required software(s) will be downloaded, and converted to `Singularity` image(s) if needed before execution of the pipeline.
Recent version of Nextflow also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images.
Images for some nf-core pipelines are available under `/sw/data/ToolBox/nf-core/` and those can be used by `NXF_SINGULARITY_CACHEDIR=/sw/data/ToolBox/nf-core/; export NXF_SINGULARITY_CACHEDIR`.
Recent version of `Nextflow` also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images.
Images for some `nf-core` pipelines are available under `/sw/data/ToolBox/nf-core/` and those can be used by `NXF_SINGULARITY_CACHEDIR=/sw/data/ToolBox/nf-core/; export NXF_SINGULARITY_CACHEDIR`.
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.
You can do this with the `--project` flag (two hyphens) when launching `Nextflow`.
For example:
```bash
@ -29,19 +29,19 @@ $ nextflow run nf-core/<PIPELINE> -profile uppmax --project snic2018-1-234 [...]
> NB: If you're not sure what your UPPMAX project ID is, try running `groups` or checking SUPR.
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.
Alternatively, you can also launch Nextflow in a `screen` or a `tmux` session.
Remember to use `-bg` to launch `Nextflow` in the background, so that the pipeline doesn't exit if you leave your terminal session.
Alternatively, you can also launch `Nextflow` in a `screen` or a `tmux` session.
## Using iGenomes references
## Using AWS 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 `conf/igenomes.config`.
A local copy of the `AWS 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 `conf/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:
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"
@ -96,7 +96,15 @@ If you use `rackham` to download the pipeline and the singularity containers, we
### Download and install Nextflow
You can use the Nextflow UPPMAX provided `module`, but if necessary, you can also download a more recent version.
You can use the `Nextflow` UPPMAX provided `module`, but if necessary, you can also download a more recent version.
```bash
# See the available versions for the module
module spider Nextflow
# Load a specific version of the Nextflow module
module load bioinfo-tools Nextflow/<VERSION>`
```
```bash
# Connect to rackham
@ -149,6 +157,19 @@ $ export NXF_SINGULARITY_CACHEDIR=/castor/project/proj_nobackup/singularity-imag
### Install nf-core tools
You can use the `nf-core` UPPMAX provided `module`, but if necessary, you can also download a more recent version.
```bash
# Connect to rackham
$ ssh -X <USER>@rackham.uppmax.uu.se
# See the available versions for the module
module spider nf-core
# Load a specific version of the nf-core module
module load bioinfo-tools nf-core/<VERSION>`
```
```bash
# Connect to rackham
$ ssh -X <USER>@rackham.uppmax.uu.se