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Merge pull request #12 from matq007/munin-config
Added configuration for Munin
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commit
de1c04ec2a
4 changed files with 55 additions and 0 deletions
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@ -60,6 +60,7 @@ Currently documentation is available for the following clusters:
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* [GIS](docs/gis.md)
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* [GIS](docs/gis.md)
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* [HEBBE](docs/hebbe.md)
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* [HEBBE](docs/hebbe.md)
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* [MENDEL](docs/mendel.md)
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* [MENDEL](docs/mendel.md)
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* [MUNIN](docs/munin.md)
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* [PHOENIX](docs/phoenix.md)
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* [PHOENIX](docs/phoenix.md)
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* [SHH](docs/shh.md)
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* [SHH](docs/shh.md)
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* [UCT_HEX](docs/uct_hex.md)
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* [UCT_HEX](docs/uct_hex.md)
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33
conf/munin.config
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33
conf/munin.config
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@ -0,0 +1,33 @@
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//Profile config names for nf-core/configs
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params {
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config_profile_name = 'MUNIN'
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config_profile_description = 'Big iron cluster profile provided by nf-core/configs.'
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config_profile_contact = 'Szilveszter Juhos (@szilva)'
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config_profile_url = ''
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}
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process {
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executor = 'local'
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}
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singularity {
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enabled = true
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autoMounts = true
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}
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// To use docker instead of singularity, use nextflow run -profile munin,docker
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docker {
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enabled = false
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mountFlags = 'z'
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fixOwnership = true
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}
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params {
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saveReference = true
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max_memory = 128.GB
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max_cpus = 16
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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 = '/data0/btb/references/igenomes/'
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}
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20
docs/munin.md
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20
docs/munin.md
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@ -0,0 +1,20 @@
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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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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 a singularity image with all of the required software before execution of the pipeline.
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Example: `nextflow run -profile munin`
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## Docker
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It is also possible to execute the pipeline using 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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A local copy of the iGenomes resource has been made available on the MUNIN cluster so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline.
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You can do this by simply using the `--genome <GENOME_ID>` parameter.
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>NB: You will need an account to use the MUNIN cluster in order to run the pipeline. If in doubt contact @szilva.
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@ -18,6 +18,7 @@ profiles {
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gis { includeConfig "${config_base}/gis.config" }
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gis { includeConfig "${config_base}/gis.config" }
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hebbe { includeConfig "${config_base}/hebbe.config" }
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hebbe { includeConfig "${config_base}/hebbe.config" }
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mendel { includeConfig "${config_base}/mendel.config" }
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mendel { includeConfig "${config_base}/mendel.config" }
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munin { includeConfig "${config_base}/munin.config" }
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phoenix { includeConfig "${config_base}/pheonix.config" }
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phoenix { includeConfig "${config_base}/pheonix.config" }
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shh { includeConfig "${config_base}/shh.config" }
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shh { includeConfig "${config_base}/shh.config" }
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uct_hex { includeConfig "${config_base}/uct_hex.config" }
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uct_hex { includeConfig "${config_base}/uct_hex.config" }
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