Merge pull request #200 from nf-core/ceh-config

Seg_globe config

.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', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'pasteur', 'phoenix', 'prince', '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', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

README.md

@@ -119,6 +119,7 @@ Currently documentation is available for the following systems:
 * [PASTEUR](docs/pasteur.md)
 * [PHOENIX](docs/phoenix.md)
 * [PRINCE](docs/prince.md)
+* [SEG_GLOBE](docs/seg_globe.md)
 * [SHH](docs/shh.md)
 * [UCT_HPC](docs/uct_hpc.md)
 * [UPPMAX](docs/uppmax.md)

conf/seg_globe.config

@@ -0,0 +1,27 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'Section for Evolutionary Genomics @ GLOBE, University of Copenhagen - seg_globe profile provided by nf-core/configs.'
+  config_profile_contact = 'Aashild Vaagene (@ashildv)'
+  config_profile_url = 'https://globe.ku.dk/research/evogenomics/'
+  max_memory = 250.GB
+  max_cpus = 35
+  max_time = 720.h
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  cacheDir = '/shared/volume/hologenomics/data/cache/nf-eager/singularity'
+}
+
+process {
+ executor = 'slurm'
+ queue = { task.time < 24.h ? 'hologenomics-short' : task.time < 168.h ? 'hologenomics' : 'hologenomics-long' }
+}
+        
+cleanup = true
+       
+executor {
+  queueSize = 8
+}
+

docs/seg_globe.md

@@ -0,0 +1,21 @@
+# nf-core/configs: Section for Evolutionary Genomics at GLOBE, Univeristy of Copenhagen (hologenomics partition on HPC) Configuration
+
+> **NB:** You will need an account to use the HPC cluster to run the pipeline. If in doubt contact IT.
+
+The profile is configured to run with Singularity version 3.6.3-1.el7 which is part of the OS installtion and does not need to be loaded as a module.
+
+Before running the pipeline you will need to load Java, miniconda and Nextflow. You can do this by including the commands below in your SLURM/sbatch script:
+
+```bash
+## Load Java and Nextflow environment modules
+module purge
+module load lib
+module load java/v1.8.0_202-jdk miniconda nextflow/v20.07.1.5412
+```
+
+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.
+The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completeed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space.
+
+This configuration will automatically choose the correct SLURM queue (short,medium,long) depending on the time and memory required by each process.
+
+> **NB:** Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be submitted from one of the login nodes.

nfcore_custom.config

@@ -38,6 +38,7 @@ profiles {
   pasteur      { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
   phoenix      { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
   prince       { includeConfig "${params.custom_config_base}/conf/prince.config" }
+  seg_globe    { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
   shh          { includeConfig "${params.custom_config_base}/conf/shh.config" }
   uct_hpc      { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }