Merge pull request #395 from ClinicalGenomicsGBG/medair

New config: Add config for Medair

.github/workflows/main.yml

@@ -66,6 +66,7 @@ jobs:
           - "jax"
           - "lugh"
           - "marvin"
+          - "medair"
           - "mjolnir_globe"
           - "maestro"
           - "mpcdf"

README.md

@@ -120,6 +120,7 @@ Currently documentation is available for the following systems:
 - [LUGH](docs/lugh.md)
 - [MAESTRO](docs/maestro.md)
 - [MARVIN](docs/marvin.md)
+- [MEDAIR](docs/medair.md)
 - [MJOLNIR_GLOBE](docs/mjolnir_globe.md)
 - [MPCDF](docs/mpcdf.md)
 - [MUNIN](docs/munin.md)

conf/medair.config

@@ -0,0 +1,46 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'Cluster profile for medair (local cluster of Clinical Genomics Gothenburg)'
+  config_profile_contact     = 'Clinical Genomics, Gothenburg (cgg-rd@gu.se, cgg-it@gu.se)'
+  config_profile_url         = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/'
+}
+
+//Nextflow parameters
+singularity {
+    enabled  = true
+    cacheDir = "/apps/bio/dependencies/nf-core/singularities"
+}
+
+profiles {
+  
+  wgs {
+    process {
+      queue                  = 'wgs.q'
+      executor               = 'sge'
+      penv                   = 'mpi'
+      process.clusterOptions = '-l excl=1'
+      params.max_cpus        = 40
+      params.max_time        = 48.h
+      params.max_memory      = 128.GB
+    }
+  }
+
+  production {
+    process {
+      queue                  = 'production.q'
+      executor               = 'sge'
+      penv                   = 'mpi'
+      process.clusterOptions = '-l excl=1'
+      params.max_cpus        = 40
+      params.max_time        = 480.h
+      params.max_memory      = 128.GB
+    }
+  }
+}
+
+//Specific parameter for pipelines that can use Sentieon (e.g. nf-core/sarek, nf-core/raredisease)
+process {
+  withLabel:'sentieon' {
+    container = "/apps/bio/singularities/sentieon-211204-peta.simg"
+  }
+}

docs/medair.md

@@ -0,0 +1,70 @@
+# nf-core/configs: Medair Configuration
+
+All nf-core pipelines have been successfully configured for use on the Medair cluster at Clinical Genomics Gothenburg.
+
+To use, run the pipeline with `-profile medair`. This will download and launch the [`medair.config`](../conf/medair.config) which has been pre-configured with a setup suitable for the Medair cluster.
+It will enable Nextflow to manage the pipeline jobs via the `SGE` job scheduler.
+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.
+
+You will need an account to use the Medair cluster in order to download or run pipelines. If in doubt, contact cgg-it.
+
+## Download nf-core pipelines
+
+### Set-up: load Nextflow and nf-core tools
+
+First you need to load relevant softwares: Nextflow and nf-core tools. You can do it as follow:
+
+```bash
+## Load Nextflow
+module load nextflow
+## Load nf-core tools
+module load miniconda
+source activate nf-core
+```
+
+### Storage of Singularity images
+
+When downloading a nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. We chose to have a central location for these images on medair: `/apps/bio/dependencies/nf-core/singularities`.
+
+For Nexflow to know where to store new images, run or add the following to your `.bashrc`:
+
+```bash
+export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities"
+```
+
+> Comment: This was also added to cronuser.
+
+### Download a pipeline
+
+We have started to download pipelines in the following location: `/apps/bio/repos/nf-core/`
+
+Use the `nf-core download --singularity-cache-only` command to start a download. It will open an interactive menu. Choose `singularity` for the software container image, and `none` for the compression type.
+
+## Run nf-core pipelines
+
+Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands below will have to be executed on one of the login nodes. If in doubt contact cgg-it (cgg-it[at]gu.se).
+
+### Set-up: load Nextflow and Singularity
+
+Before running a pipeline you will need to load Nextflow and Singularity using the environment module system on Medair. You can do this by issuing the commands below:
+
+```bash
+## Load Nextflow and Singularity environment modules
+module purge
+module load nextflow
+module load singularity
+```
+
+### Choose a profile
+
+Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 days, versus 2 days for the `wgs` profile).
+
+For example, the following job would run with the `wgs` profile:
+
+```bash
+run nextflow nf-core/raredisease -profile medair,wgs
+```
+
+### Sentieon
+
+In some pipelines (sarek, raredisease) it is possible to use Sentieon for alignment and variant calling. If ones uses the label `sentieon` for running a process, the config file contains the path to the Sentieon singularity image on Medair.

nfcore_custom.config

@@ -49,6 +49,7 @@ profiles {
   lugh         { includeConfig "${params.custom_config_base}/conf/lugh.config" }
   maestro      { includeConfig "${params.custom_config_base}/conf/maestro.config" }
   marvin       { includeConfig "${params.custom_config_base}/conf/marvin.config" }
+  medair       { includeConfig "${params.custom_config_base}/conf/medair.config" }
   mjolnir_globe { includeConfig "${params.custom_config_base}/conf/mjolnir_globe.config" }
   mpcdf        { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
   munin        { includeConfig "${params.custom_config_base}/conf/munin.config" }