diff --git a/conf/munin.config b/conf/munin.config index bca56f7..52062e5 100644 --- a/conf/munin.config +++ b/conf/munin.config @@ -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/' } diff --git a/docs/munin.md b/docs/munin.md index 17233bb..167ff9b 100644 --- a/docs/munin.md +++ b/docs/munin.md @@ -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