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Merge pull request #258 from ameynert/master

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Update eddie config docs & added viralrecon config
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Harshil Patel 2021-07-22 15:14:54 +01:00 committed by GitHub
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13
conf/pipeline/viralrecon/eddie.config Normal file
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@ -0,0 +1,13 @@
env {
BLASTDB_LMDB_MAP_SIZE=100000000
}
process {
withName : '.*PICARD.*' {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName : '.*SNPEFF.*' {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
}

16
docs/eddie.md
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# nf-core/configs: Eddie Configuration # nf-core/configs: Eddie Configuration
nf-core pipelines sarek, rnaseq, and atacseq have all been tested on the University of Edinburgh Eddie HPC. nf-core pipelines sarek, rnaseq, atacseq, and viralrecon have all been tested on the University of Edinburgh Eddie HPC. All except atacseq have pipeline-specific config files; atacseq does not yet support this.
## Getting help ## Getting help
There is a Slack channel dedicated to eddie users on the MRC IGMM Slack: [https://igmm.slack.com/channels/eddie3](https://igmm.slack.com/channels/eddie3) There is a Slack channel dedicated to eddie users on the MRC IGC Slack: [https://igmm.slack.com/channels/eddie3](https://igmm.slack.com/channels/eddie3)
## Using the Eddie config profile ## Using the Eddie config profile
@ -35,13 +35,13 @@ This config enables Nextflow to manage the pipeline jobs via the SGE job schedul
## Singularity set-up ## Singularity set-up
Load Singularity from the module system and, if you have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to the NextGenResources path below. If some containers for your pipeline run are not present, please contact the [IGMM Data Manager](data.manager@igmm.ed.ac.uk) to have them added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline. Load Singularity from the module system and, if you have access to `/exports/igmm/eddie/BioinformaticsResources`, set the Singularity cache directory to the BioinformaticsResources path below. If some containers for your pipeline run are not present, please contact the [IGC Data Manager](data.manager@igc.ed.ac.uk) to have them added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline.
If you do not have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again. If you do not have access to `/exports/igmm/eddie/BioinformaticsResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again.
```bash ```bash
module load singularity module load singularity
export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/NextGenResources/nextflow/singularity" export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/BioinformaticsResources/nf-core/singularity-images"
``` ```
Singularity will create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations. Singularity will create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations.
@ -68,7 +68,7 @@ If your eddie terminal disconnects your Nextflow job will stop. You can run Next
nohup ./nextflow_run.sh & nohup ./nextflow_run.sh &
``` ```
### On a wild west node - IGMM only ### On a wild west node - IGC only
Wild west nodes on eddie can be accessed via ssh (node2c15, node2c16, node3g22). To run Nextflow on one of these nodes, do it within a [screen session](https://linuxize.com/post/how-to-use-linux-screen/). Wild west nodes on eddie can be accessed via ssh (node2c15, node2c16, node3g22). To run Nextflow on one of these nodes, do it within a [screen session](https://linuxize.com/post/how-to-use-linux-screen/).
@ -92,12 +92,12 @@ screen -r <session_name>
## Using iGenomes references ## Using iGenomes references
A local copy of the iGenomes resource has been made available on the Eddie HPC for those with access to `/exports/igmm/eddie/NextGenResources` so you should be able to run the pipeline against any reference available in the `igenomes.config`. A local copy of the iGenomes resource has been made available on the Eddie HPC for those with access to `/exports/igmm/eddie/BioinformaticsResources` 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. You can do this by simply using the `--genome <GENOME_ID>` parameter.
## Adjusting maximum resources ## Adjusting maximum resources
This config is set for IGMM standard nodes which have 32 cores and 384GB memory. If you are a non-IGMM user, please see the [ECDF specification](https://www.wiki.ed.ac.uk/display/ResearchServices/Memory+Specification) and adjust the `--clusterOptions` flag appropriately, e.g. This config is set for IGC standard nodes which have 32 cores and 384GB memory. If you are a non-IGC user, please see the [ECDF specification](https://www.wiki.ed.ac.uk/display/ResearchServices/Memory+Specification) and adjust the `--clusterOptions` flag appropriately, e.g.
```bash ```bash
--clusterOptions "-C mem256GB" --max_memory "256GB" --clusterOptions "-C mem256GB" --max_memory "256GB"

4
pipeline/viralrecon.config
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@ -5,3 +5,7 @@
*/ */
includeConfig "${params.custom_config_base}/conf/pipeline/viralrecon/genomes.config" includeConfig "${params.custom_config_base}/conf/pipeline/viralrecon/genomes.config"
profiles {
eddie { includeConfig "${params.custom_config_base}/conf/pipeline/viralrecon/eddie.config" }
}