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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'
}
sngularity {
enabled = true
autoMounts = true
}
params {
saveReference = true
max_memory = 256.GB
max_memory = 128.GB
max_cpus = 16
max_time = 72.h
// illumina iGenomes reference file paths on UPPMAX

23
docs/munin.md
View file

@ -2,28 +2,7 @@
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
}
```
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.
## Below are non-mandatory information on iGenomes specific configuration