Merge pull request #212 from noirot/master

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

conf/ifb_core.config

@@ -0,0 +1,24 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'The IFB core cluster profile'
+  config_profile_contact = 'https://community.france-bioinformatique.fr'
+  config_profile_url = 'https://www.france-bioinformatique.fr/'
+}
+
+singularity {
+  // need one image per execution
+  enabled = true
+  runOptions = '-B /shared'
+}
+
+process {
+  executor = 'slurm'
+}
+
+params {
+  igenomes_ignore = true
+  // Max resources requested by a normal node on genotoul.
+  max_memory = 240.GB
+  max_cpus = 28
+  max_time = 96.h
+}

docs/ifb_core.md

@@ -0,0 +1,40 @@
+# nf-core/configs: IFB core Configuration
+
+All nf-core pipelines have been successfully configured for use on the cluster of the IFB (Institut Francais de Bioinformatique).
+
+To use, run the pipeline with `-profile ifb_core`. This will download and launch the [`ifb_core.config`](../conf/ifb_core.config) which has been pre-configured with a setup suitable for the IFB core 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.
+
+## How to use on IFB core
+
+Before running the pipeline you will need to load Nextflow using the environment module system on IFB core. You can do this by issuing the commands below:
+
+```bash
+# Login to a compute node
+srun --pty bash
+
+## Load Nextflow and Singularity environment modules
+module purge
+module load nextflow/20.04.1
+
+# Run a downloaded/git-cloned nextflow workflow from
+nextflow run \\
+nf-core/workflow \\
+-resume
+-profile ifb_core \\
+--email my-email@example.org  \\
+-c my-specific.config
+...
+
+
+# Or use the nf-core client
+nextflow run nf-core/rnaseq ...
+
+```
+
+## Databanks
+
+A local copy of several genomes are available in `/shared/bank` directory. See
+our [databank page](https://ifb-elixirfr.gitlab.io/cluster/doc/banks/)
+to search for your favorite genome.
+
+>NB: You will need an account to use the HPC cluster on IFB core in order to run the pipeline. If in doubt contact IT or go to [account page](https://my.cluster.france-bioinformatique.fr/manager2/login).

nfcore_custom.config

@@ -24,6 +24,7 @@ profiles {
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
   ebc          { includeConfig "${params.custom_config_base}/conf/ebc.config" }
   icr_davros   { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
+  ifb_core     { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
   imperial     { includeConfig "${params.custom_config_base}/conf/imperial.config" }
   imperial_mb  { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }  
   genotoul     { includeConfig "${params.custom_config_base}/conf/genotoul.config" }