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fix: update and rearrange munin configuration file and docs

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MaxUlysse 2019-08-07 11:10:48 +02:00
parent da2a9047b0
commit 332ba0dadb
2 changed files with 15 additions and 11 deletions
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20
conf/munin.config
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@ -1,20 +1,22 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { 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_contact = 'Szilveszter Juhos (@szilva)'
config_profile_url = '' config_profile_url = ''
} }
process { process {
executor = 'local' executor = 'local'
maxForks = 48
} }
// To use docker, use nextflow run -profile munin,singularity
singularity { singularity {
enabled = true enabled = true
autoMounts = 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 { docker {
enabled = false enabled = false
mountFlags = 'z' mountFlags = 'z'
@ -22,11 +24,11 @@ docker {
} }
params { params {
saveReference = true // general params
max_memory = 754.GB
max_memory = 128.GB max_cpus = 48
max_cpus = 16
max_time = 72.h max_time = 72.h
// illumina iGenomes reference file paths on UPPMAX
igenomes_base = '/data1/references/igenomes/' // AWS iGenomes reference file paths on munin
} igenome_base = '/data1/references/igenomes/'
}

6
docs/munin.md
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@ -1,8 +1,10 @@
# nf-core/configs: MUNIN Configuration # 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. 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.
Example: `nextflow run -profile munin` Example: `nextflow run -profile munin`