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Updated munin doc and configuration

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Martin Proks 2019-01-10 15:46:16 +01:00
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@ -60,6 +60,7 @@ Currently documentation is available for the following clusters:
* [GIS](docs/gis.md)
* [HEBBE](docs/hebbe.md)
* [MENDEL](docs/mendel.md)
* [MUNIN](docs/munin.md)
* [PHOENIX](docs/phoenix.md)
* [SHH](docs/shh.md)
* [UCT_HEX](docs/uct_hex.md)

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@ -14,7 +14,7 @@ params {
saveReference = true
max_memory = 256.GB
max_cpus = 32
max_cpus = 16
max_time = 72.h
// illumina iGenomes reference file paths on UPPMAX
igenomes_base = '/data0/btb/references/igenomes/'

33
docs/munin.md Normal file
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@ -0,0 +1,33 @@
# nf-core/configs: MUNIN Configuration
All nf-core pipelines have been successfully configured for use on the MUNIN cluster aka big iron.
To use, run the pipeline with `-profile munin`. This will download and launch the [`munin.config`](../conf/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster. Using this profile, Nextflow will download either docker or singularity image with all of the required software before execution of the pipeline.
## Running pipeline with Docker
>NB: Make sure when running pipeline using docker to be in docker group
```groovy
// https://github.com/nextflow-io/nextflow/issues/572
docker {
mountFlags = 'z'
fixOwnership = true
}
```
## Running pipeline with Singularity
```groovy
// https://github.com/nextflow-io/nextflow/issues/572
singularity {
autoMounts = true
}
```
## Below are non-mandatory information on iGenomes specific configuration
A local copy of the iGenomes resource has been made available on MUNIN cluster so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline.
You can do this by simply using the `--genome <GENOME_ID>` parameter.
>NB: You will need an account to use the munin cluster in order to run the pipeline. If in doubt contact @szilva.

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@ -18,6 +18,7 @@ profiles {
gis { includeConfig "${config_base}/gis.config" }
hebbe { includeConfig "${config_base}/hebbe.config" }
mendel { includeConfig "${config_base}/mendel.config" }
munin { includeConfig "${config_base}/munin.config" }
phoenix { includeConfig "${config_base}/pheonix.config" }
shh { includeConfig "${config_base}/shh.config" }
uct_hex { includeConfig "${config_base}/uct_hex.config" }