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Merge pull request #65 from MaxUlysse/master

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fix: update and rearrange munin configuration file and docs
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Szilveszter Juhos 2019-08-16 11:06:32 +02:00 committed by GitHub
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19
conf/munin.config
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@ -1,20 +1,21 @@
//Profile config names for nf-core/configs
params {
config_profile_description = 'Big iron cluster profile provided by nf-core/configs.'
config_profile_description = 'MUNIN profile provided by nf-core/configs.'
config_profile_contact = 'Szilveszter Juhos (@szilva)'
config_profile_url = ''
}
process {
executor = 'local'
maxForks = 46
}
// To use singularity, use nextflow run -profile munin,singularity
singularity {
enabled = true
autoMounts = true
}
// To use docker instead of singularity, use nextflow run -profile munin,docker
// To use docker, use nextflow run -profile munin,docker
docker {
enabled = false
mountFlags = 'z'
@ -22,11 +23,11 @@ docker {
}
params {
saveReference = true
max_memory = 128.GB
max_cpus = 16
// general params
max_memory = 752.GB
max_cpus = 46
max_time = 72.h
// illumina iGenomes reference file paths on UPPMAX
igenomes_base = '/data1/references/igenomes/'
// Local AWS iGenomes reference file paths on munin
igenome_base = '/data1/references/igenomes/'
}

22
docs/munin.md
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@ -1,15 +1,31 @@
# nf-core/configs: MUNIN Configuration
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.
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, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
## Usage
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.
Example: `nextflow run -profile munin`
## Docker
### Singularity
This is the default behavior of this configuration profile.
Using this profile, if no singularity image are available, one will be downloaded from dockerhub, and converted to a Singularity image before execution of the pipeline.
It is also possible to specify the singularity profile:
Example: `nextflow run -profile munin,singularity`
### Docker
It is also possible to execute the pipeline using Docker.
Using this profile, if no docker image are available, one will be downloaded from dockerhub before execution of the pipeline.
Example: `nextflow run -profile munin,docker`
## Below are non-mandatory information on iGenomes specific configuration