Merge pull request #365 from rajewski/master

Cedars-Sinai HPC

.github/workflows/main.yml

@@ -43,6 +43,7 @@ jobs:
           - "cbe"
           - "ccga_dx"
           - "ccga_med"
+          - "cedars"
           - "cfc"
           - "cfc_dev"
           - "cheaha"

README.md

@@ -99,6 +99,7 @@ Currently documentation is available for the following systems:
 - [CBE](docs/cbe.md)
 - [CCGA_DX](docs/ccga_dx.md)
 - [CCGA_MED](docs/ccga_med.md)
+- [Cedars-Sinai](docs/cedars.md)
 - [CFC](docs/cfc.md)
 - [CHEAHA](docs/cheaha.md)
 - [Computerome](docs/computerome.md)

conf/cedars.config

@@ -0,0 +1,26 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'Cedars-Sinai Medical Center HPC Profile'
+  config_profile_contact = 'Alex Rajewski (@rajewski)'
+  config_profile_url = 'https://www.cedars-sinai.edu/research/cores/informatics-computing/resources.html'
+  max_memory = 90.GB
+  max_cpus = 10
+  max_time = 240.h
+}
+
+// Specify the queing system
+executor {
+  name = "sge"
+}
+
+process {
+  penv = 'smp'
+  beforeScript =
+  """
+  module load 'singularity/3.6.0'
+  """
+}
+
+singularity {
+  enabled = true
+}

docs/cedars.md

@@ -0,0 +1,7 @@
+# Cedars-Sinai Medical Center HPC
+
+  - You will need HPC access from EIS, which can be requested in the Service Center.
+  - You will need to load the nextflow module on the HPC before running any pipelines (`module load nextflow`). This should automatically load Java as well.
+  - Run this with `-profile cedars`
+  - By default this config file does not specify a queue for submission, and things will thus go to `all.q`. Because of that, the memory and cpu limits have been set accordingly.
+  - We  highly recommend specifying a location of a cache directory to store singularity images (so you re-use them across runs, and not pull each time), by specifying the location with the `$NXF_SINGULARITY_CACHE_DIR` bash environment variable in your `.bash_profile` or `.bashrc`

nfcore_custom.config

@@ -24,6 +24,7 @@ profiles {
   cbe          { includeConfig "${params.custom_config_base}/conf/cbe.config" }
   ccga_dx      { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
   ccga_med     { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }
+  cedars       { includeConfig "${params.custom_config_base}/conf/cedars.config" }
   cfc          { includeConfig "${params.custom_config_base}/conf/cfc.config" }
   cfc_dev      { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" }
   cheaha       { includeConfig "${params.custom_config_base}/conf/cheaha.config" }