Merge pull request #12 from matq007/munin-config

Added configuration for Munin

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)

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/'
+}

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 <GENOME_ID>` parameter.
+
+>NB: You will need an account to use the MUNIN cluster in order to run the pipeline. If in doubt contact @szilva.

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" }