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Merge pull request #65 from MaxUlysse/master
fix: update and rearrange munin configuration file and docs
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commit
e5d8f20204
2 changed files with 29 additions and 12 deletions
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@ -1,20 +1,21 @@
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//Profile config names for nf-core/configs
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//Profile config names for nf-core/configs
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params {
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params {
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config_profile_description = 'Big iron cluster profile provided by nf-core/configs.'
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config_profile_description = 'MUNIN profile provided by nf-core/configs.'
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config_profile_contact = 'Szilveszter Juhos (@szilva)'
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config_profile_contact = 'Szilveszter Juhos (@szilva)'
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config_profile_url = ''
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config_profile_url = ''
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}
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}
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process {
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process {
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executor = 'local'
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executor = 'local'
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maxForks = 46
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}
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}
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// To use singularity, use nextflow run -profile munin,singularity
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singularity {
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singularity {
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enabled = true
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enabled = true
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autoMounts = true
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}
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}
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// To use docker instead of singularity, use nextflow run -profile munin,docker
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// To use docker, use nextflow run -profile munin,docker
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docker {
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docker {
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enabled = false
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enabled = false
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mountFlags = 'z'
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mountFlags = 'z'
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@ -22,11 +23,11 @@ docker {
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}
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}
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params {
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params {
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saveReference = true
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// general params
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max_memory = 752.GB
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max_memory = 128.GB
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max_cpus = 46
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max_cpus = 16
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max_time = 72.h
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max_time = 72.h
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// illumina iGenomes reference file paths on UPPMAX
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igenomes_base = '/data1/references/igenomes/'
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// Local AWS iGenomes reference file paths on munin
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igenome_base = '/data1/references/igenomes/'
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}
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}
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@ -1,15 +1,31 @@
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# nf-core/configs: MUNIN Configuration
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# nf-core/configs: MUNIN Configuration
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All nf-core pipelines have been successfully configured for use on the MUNIN cluster aka big iron.
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All nf-core pipelines have been successfully configured for use on the MUNIN cluster.
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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.
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## Usage
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To use, run the pipeline with `-profile munin`.
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This will download and launch the [`munin.config`](../conf/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster.
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Example: `nextflow run -profile munin`
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Example: `nextflow run -profile munin`
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## Docker
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### Singularity
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This is the default behavior of this configuration profile.
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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.
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It is also possible to specify the singularity profile:
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Example: `nextflow run -profile munin,singularity`
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### Docker
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It is also possible to execute the pipeline using Docker.
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It is also possible to execute the pipeline using Docker.
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Using this profile, if no docker image are available, one will be downloaded from dockerhub before execution of the pipeline.
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Example: `nextflow run -profile munin,docker`
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Example: `nextflow run -profile munin,docker`
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## Below are non-mandatory information on iGenomes specific configuration
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## Below are non-mandatory information on iGenomes specific configuration
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