Merge pull request #346 from sagc-bioinformatics/sahmri

Added SAHMRI profile

.github/workflows/main.yml

@@ -76,6 +76,7 @@ jobs:
             - 'phoenix'
             - 'prince'
             - 'rosalind'
+            - 'sahmri'
             - 'sanger'
             - 'seg_globe'
             - 'uct_hpc'

conf/sahmri.config

@@ -0,0 +1,34 @@
+params {
+  config_profile_description = 'South Australian Health and Medical Research Institute (SAHMRI) HPC cluster profile.'
+  config_profile_contact     = 'Nathan Watson-Haigh (nathan.watson-haigh@sahmri.com)'
+  config_profile_url         = "https://sahmri.org.au"
+  max_memory      = 375.GB
+  max_cpus        = 32
+  max_time        = 14.d
+  igenomes_base   = '/cancer/storage/shared/igenomes/references/'
+}
+process {
+  executor        = 'slurm'
+  queue           = 'sahmri_prod_hpc,sahmri_cancer_hpc'
+  maxRetries      = 2
+
+  cpus            = { check_max( 2 * task.attempt, 'cpus') }
+  memory          = { check_max( 1.GB * task.attempt, 'memory') }
+  time            = { check_max( 10.m * task.attempt, 'time') }
+}
+executor {
+  queueSize       = 50
+  submitRateLimit = '10 sec'
+}
+singularity {
+  enabled         = true
+  autoMounts      = true
+  beforeScript    = 'export PATH=/apps/opt/singularity/latest/bin:${PATH}'
+  cacheDir        = '/cancer/storage/shared/simg'
+}
+cleanup = true
+profiles {
+  debug {
+    cleanup = false
+  }
+}

docs/sahmri.md

@@ -0,0 +1,18 @@
+# nf-core/configs: SAHMRI HPC Configuration
+
+All nf-core pipelines have been successfully configured for use on the HPC cluster at [SAHMRI](https://sahmri.org.au/).  
+To use, run the pipeline with `-profile sahmri`. This will download and launch the [`sahmri.config`](../conf/sahmri.config) which has been pre-configured
+with a setup suitable for the SAHMRI HPC cluster. Using this profile, either a docker image containing all of the required software will be downloaded,
+and converted to a Singularity image or a Singularity image downloaded directly before execution of the pipeline.  
+
+The latest version of Nextflow is not installed by default on the SAHMRI HPC cluster. You will need to install it into a directory you have write access to.
+Follow these instructions from the Nextflow documentation.
+
+- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
+
+All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline
+has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
+
+> NB: You will need an account to use the SAHMRI HPC cluster in order to run the pipeline. If in doubt contact the ICT Service Desk.
+> NB: Nextflow will need to submit the jobs via SLURM to the SAHMRI HPC cluster and as such the commands above will have to be executed on the login
+node. If in doubt contact ICT.

nfcore_custom.config

@@ -57,6 +57,7 @@ profiles {
   phoenix      { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
   prince       { includeConfig "${params.custom_config_base}/conf/prince.config" }
   rosalind     { includeConfig "${params.custom_config_base}/conf/rosalind.config" }
+  sahmri       { includeConfig "${params.custom_config_base}/conf/sahmri.config" }
   sanger       { includeConfig "${params.custom_config_base}/conf/sanger.config"}
   seg_globe    { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
   uct_hpc      { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }