diff --git a/README.md b/README.md index cce1ed2..6d5b340 100644 --- a/README.md +++ b/README.md @@ -60,6 +60,7 @@ Currently documentation is available for the following clusters: * [GIS](docs/gis.md) * [HEBBE](docs/hebbe.md) * [MENDEL](docs/mendel.md) +* [MUNIN](docs/munin.md) * [PHOENIX](docs/phoenix.md) * [SHH](docs/shh.md) * [UCT_HEX](docs/uct_hex.md) diff --git a/conf/munin.config b/conf/munin.config new file mode 100644 index 0000000..a24929e --- /dev/null +++ b/conf/munin.config @@ -0,0 +1,33 @@ +//Profile config names for nf-core/configs +params { + config_profile_name = 'MUNIN' + config_profile_description = 'Big iron cluster profile provided by nf-core/configs.' + config_profile_contact = 'Szilveszter Juhos (@szilva)' + config_profile_url = '' +} + +process { + executor = 'local' +} + +singularity { + enabled = true + autoMounts = true +} + +// To use docker instead of singularity, use nextflow run -profile munin,docker +docker { + enabled = false + mountFlags = 'z' + fixOwnership = true +} + +params { + saveReference = true + + max_memory = 128.GB + max_cpus = 16 + max_time = 72.h + // illumina iGenomes reference file paths on UPPMAX + igenomes_base = '/data0/btb/references/igenomes/' +} diff --git a/docs/munin.md b/docs/munin.md new file mode 100644 index 0000000..bde7f2e --- /dev/null +++ b/docs/munin.md @@ -0,0 +1,20 @@ +# nf-core/configs: MUNIN Configuration + +All nf-core pipelines have been successfully configured for use on the MUNIN cluster aka big iron. + +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. + +Example: `nextflow run -profile munin` + +## Docker + +It is also possible to execute the pipeline using Docker. + +Example: `nextflow run -profile munin,docker` + +## Below are non-mandatory information on iGenomes specific configuration + +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. +You can do this by simply using the `--genome ` parameter. + +>NB: You will need an account to use the MUNIN cluster in order to run the pipeline. If in doubt contact @szilva. diff --git a/nfcore_custom.config b/nfcore_custom.config index 7a08d3e..757b70b 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -18,6 +18,7 @@ profiles { gis { includeConfig "${config_base}/gis.config" } hebbe { includeConfig "${config_base}/hebbe.config" } mendel { includeConfig "${config_base}/mendel.config" } + munin { includeConfig "${config_base}/munin.config" } phoenix { includeConfig "${config_base}/pheonix.config" } shh { includeConfig "${config_base}/shh.config" } uct_hex { includeConfig "${config_base}/uct_hex.config" }