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Setting Singularity as default method

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Martin Proks 2019-01-11 14:37:12 +01:00
parent 548c8bca3f
commit 89dbb6c061
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2 changed files with 7 additions and 23 deletions
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7
conf/munin.config
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@ -10,10 +10,15 @@ process {
executor = 'local' executor = 'local'
} }
sngularity {
enabled = true
autoMounts = true
}
params { params {
saveReference = true saveReference = true
max_memory = 256.GB max_memory = 128.GB
max_cpus = 16 max_cpus = 16
max_time = 72.h max_time = 72.h
// illumina iGenomes reference file paths on UPPMAX // illumina iGenomes reference file paths on UPPMAX

23
docs/munin.md
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@ -2,28 +2,7 @@
All nf-core pipelines have been successfully configured for use on the MUNIN cluster aka big iron. 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. 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 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 ## Below are non-mandatory information on iGenomes specific configuration