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feat: more details
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@ -8,18 +8,18 @@ We have a Slack channel dedicated to UPPMAX users on the nf-core Slack: [https:/
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## Using the UPPMAX config profile
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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`).
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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`).
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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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It will enable Nextflow to manage the pipeline jobs via the Slurm job scheduler.
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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.
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It will enable `Nextflow` to manage the pipeline jobs via the `Slurm` job scheduler.
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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.
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Recent version of Nextflow also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images.
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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`.
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Recent version of `Nextflow` also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images.
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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`.
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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.
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You can do this with the `--project` flag (two hyphens) when launching `Nextflow`.
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For example:
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```bash
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@ -29,19 +29,19 @@ $ nextflow run nf-core/<PIPELINE> -profile uppmax --project snic2018-1-234 [...]
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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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Just run Nextflow on a login node and it will handle everything else.
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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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Alternatively, you can also launch Nextflow in a `screen` or a `tmux` session.
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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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Alternatively, you can also launch `Nextflow` in a `screen` or a `tmux` session.
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## Using iGenomes references
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## Using AWS 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 `conf/igenomes.config`.
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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`.
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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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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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@ -96,7 +96,15 @@ If you use `rackham` to download the pipeline and the singularity containers, we
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### Download and install Nextflow
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You can use the Nextflow UPPMAX provided `module`, but if necessary, you can also download a more recent version.
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You can use the `Nextflow` UPPMAX provided `module`, but if necessary, you can also download a more recent version.
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```bash
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# See the available versions for the module
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module spider Nextflow
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# Load a specific version of the Nextflow module
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module load bioinfo-tools Nextflow/<VERSION>`
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```
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```bash
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# Connect to rackham
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@ -149,6 +157,19 @@ $ export NXF_SINGULARITY_CACHEDIR=/castor/project/proj_nobackup/singularity-imag
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### Install nf-core tools
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You can use the `nf-core` UPPMAX provided `module`, but if necessary, you can also download a more recent version.
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```bash
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# Connect to rackham
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$ ssh -X <USER>@rackham.uppmax.uu.se
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# See the available versions for the module
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module spider nf-core
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# Load a specific version of the nf-core module
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module load bioinfo-tools nf-core/<VERSION>`
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```
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```bash
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# Connect to rackham
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$ ssh -X <USER>@rackham.uppmax.uu.se
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