Merge pull request #216 from asafpr/master

Added JAX conf

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
+          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

README.md

@@ -113,6 +113,7 @@ Currently documentation is available for the following systems:
 * [GOOGLE](docs/google.md)
 * [HEBBE](docs/hebbe.md)
 * [ICR_DAVROS](docs/icr_davros.md)
+* [JAX](docs/jax.md)
 * [KRAKEN](docs/kraken.md)
 * [MPCDF](docs/mpcdf.md)
 * [MUNIN](docs/munin.md)

conf/jax.config

@@ -0,0 +1,21 @@
+params {
+      config_profile_description = 'The Jackson Laboratory Sumner HPC profile provided by nf-core/configs.'
+      config_profile_contact = 'Asaf Peer (@peera)'
+      config_profile_url = 'https://jacksonlaboratory.sharepoint.com/sites/ResearchIT/SitePages/Welcome-to-Sumner.aspx'
+    }
+
+executor.$slurm.queueSize = 250
+process {
+    executor = "slurm"
+    queue = "compute"
+    clusterOptions = {task.time < 72.h ? '-q batch' : '-q long'}
+    module = "slurm"
+    beforeScript = 'module load singularity'
+}
+singularity.enabled = true
+singularity.autoMounts = true
+params {
+      max_memory = 768.GB
+      max_cpus = 70
+      max_time = 336.h
+    }

docs/jax.md

@@ -0,0 +1,8 @@
+# nf-core/configs: JAX Configuration
+
+All nf-core pipelines have been successfully configured for use on the JAX Sumner cluster at The Jackson Laboratory.
+
+To use, run the pipeline with `-profile jax`. This will download and launch the [`jax.config`](../conf/jax.config) which has been pre-configured with a setup suitable for JAX Sumner cluster. 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 and slurm will be used as well.
+
+>NB: You will need an account to use the HPC cluster JAX in order to run the pipeline. If in doubt contact IT.
+>NB: Nextflow should not be executed on the login nodes. If in doubt contact IT.

nfcore_custom.config

@@ -46,6 +46,7 @@ profiles {
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
   utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
   uzh          { includeConfig "${params.custom_config_base}/conf/uzh.config" }
+  jax          { includeConfig "${params.custom_config_base}/conf/jax.config" }
 }
 
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