Merge branch 'master' into master

README.md

@@ -97,10 +97,9 @@ Currently documentation is available for the following systems:
 * [BIGPURPLE](docs/bigpurple.md)
 * [BINAC](docs/binac.md)
 * [CBE](docs/cbe.md)
-* [CCGA](docs/ccga.md)
 * [CCGA_DX](docs/ccga_dx.md)
 * [CCGA_MED](docs/ccga_med.md)
-* [CFC](docs/binac.md)
+* [CFC](docs/cfc.md)
 * [CRICK](docs/crick.md)
 * [CZBIOHUB_AWS](docs/czbiohub.md)
 * [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)

conf/ccga.config

@@ -1,41 +0,0 @@
-//Profile config names for nf-core/configs
-params {
-  config_profile_description = 'CCGA cluster profile provided by nf-core/configs.'
-  config_profile_contact = 'Marc Hoeppner (@marchoeppner)'
-  config_profile_url = 'https://www.ccga.uni-kiel.de/'
-}
-
-/*
- * -------------------------------------------------
- *  Nextflow config file for CCGA cluster in Kiel
- * -------------------------------------------------
- */
-
-singularity {
-  enabled = true
-  runOptions = "-B /ifs -B /scratch -B /work_beegfs"
-  cacheDir = "/ifs/data/nfs_share/ikmb_repository/singularity_cache/"
-}
-
-executor {
-  queueSize=100
-}
-
-process {
-
-  // Global process config
-  executor = 'slurm'
-  queue = 'ikmb_a'
-
-  clusterOptions = { "--qos=ikmb_a" }
-
-}
-
-params {
-  // illumina iGenomes reference file paths on RZCluster
-  igenomes_base = '/ifs/data/nfs_share/ikmb_repository/references/iGenomes/references/'
-  saveReference = true
-  max_memory = 128.GB
-  max_cpus = 16
-  max_time = 120.h
-}

conf/cfc.config

@@ -13,6 +13,7 @@ singularity {
 process {
   beforeScript = 'module load devel/singularity/3.4.2'
   executor = 'slurm'
+  queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' }
 }
 
 weblog{
@@ -22,7 +23,7 @@ weblog{
 
 params {
   igenomes_base = '/nfsmounts/igenomes'
-  max_memory = 498.GB
+  max_memory = 1999.GB
-  max_cpus = 20
+  max_cpus = 128
   max_time = 140.h
 }

docs/ccga.md

@@ -1,18 +0,0 @@
-# nf-core/configs: CCGA Configuration
-
-Deployment and testing of nf-core pipelines at the CCGA cluster is on-going.
-
-To use, run the pipeline with `-profile ccga`. This will download and launch the [`ccga.config`](../conf/ccga.config) which has been pre-configured with a setup suitable for the CCGA 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.
-
-Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on the cluster. You can do this by issuing the commands below:
-
-```bash
-## Load Nextflow and Singularity environment modules
-module purge
-module load IKMB
-module load Java/1.8.0
-module load Nextflow
-module load singularity3.1.0
-```
-
->NB: Access to the CCGA cluster is restricted to IKMB/CCGA employes. Please talk to Marc Hoeppner to get access (@marchoeppner).

docs/cfc.md

@@ -10,8 +10,11 @@ Before running the pipeline you will need to load Nextflow and Singularity using
 ## Load Nextflow and Singularity environment modules
 module purge
 module load devel/java_jdk/1.8.0u121
-module load qbic/singularity_slurm/3.0.3
+module load devel/singularity/3.4.2
 ```
 
 >NB: You will need an account to use the HPC cluster CFC in order to run the pipeline. If in doubt contact IT.
 >NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.
+New  HighMem nodes are available on the cfc, Partition/queue name is qbic, each node has 128Cores and 2TB of RAM.
+The old queue (Name compute) is set to default by slurm.
+Each process over 60GB of RAM or over 20cpus should run on those new nodes.

nfcore_custom.config

@@ -14,7 +14,6 @@ profiles {
   bigpurple    { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
   binac        { includeConfig "${params.custom_config_base}/conf/binac.config" }
   cbe          { includeConfig "${params.custom_config_base}/conf/cbe.config" }
-  ccga         { includeConfig "${params.custom_config_base}/conf/ccga.config" }
   ccga_dx      { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
   ccga_med     { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }
   cfc          { includeConfig "${params.custom_config_base}/conf/cfc.config" }