Merge pull request #57 from marchoeppner/dev

Adding CCGA DX cluster config

README.md

@@ -85,6 +85,7 @@ Currently documentation is available for the following clusters:
 * [BINAC](docs/binac.md)
 * [BIGPURPLE](docs/bigpurple.md)
 * [CCGA](docs/ccga.md)
+* [CCGA_DX](/docs/ccga_dx.md)
 * [CFC](docs/binac.md)
 * [CRICK](docs/crick.md)
 * [GIS](docs/gis.md)

conf/ccga_dx.config

@@ -0,0 +1,37 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'CCGA DX 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
+}
+
+executor {
+  queueSize=100
+}
+
+process {
+
+  // Global process config
+  executor = 'slurm'
+  queue = 'htc'
+
+}
+
+params {
+  // illumina iGenomes reference file paths on DX Cluster
+  igenomes_base = '/mnt/ld_ng_out/sukmb352/references/iGenomes/references/'
+  saveReference = true
+  max_memory = 250.GB
+  max_cpus = 20
+  max_time = 240.h
+}

docs/ccga_dx.md

@@ -0,0 +1,9 @@
+# nf-core/configs: CCGA DX Configuration
+
+Deployment and testing of nf-core pipelines at the CCGA DX cluster is on-going. 
+
+To use, run the pipeline with `-profile ccga_dx`. This will download and launch the [`ccga_dx.config`](../conf/ccga_dx.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 have Nextflow installed. 
+
+>NB: Access to the CCGA DX cluster is restricted to IKMB/CCGA employes. Please talk to Marc Hoeppner to get access (@marchoeppner).

nfcore_custom.config

@@ -14,6 +14,7 @@ params.custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/$
 profiles {
   binac        { includeConfig "${params.custom_config_base}/conf/binac.config" }
   ccga         { includeConfig "${params.custom_config_base}/conf/ccga.config" }
+  ccga_dx      { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
   cfc          { includeConfig "${params.custom_config_base}/conf/cfc.config" }
   crick        { includeConfig "${params.custom_config_base}/conf/crick.config" }
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }