Merge pull request #67 from phue/cbe_profile

add cbe config

.travis.yml

@@ -27,4 +27,4 @@ script:
       tr -s ' ' | \
       cut -d " " -f 2 | \
       grep -v "czbiohub_aws" | \
-      xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {}
+      xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf --custom_config_base=${TRAVIS_BUILD_DIR} -profile {}

README.md

@@ -84,6 +84,7 @@ Currently documentation is available for the following clusters:
 
 * [BIGPURPLE](docs/bigpurple.md)
 * [BINAC](docs/binac.md)
+* [CBE](docs/cbe.md)
 * [CCGA](docs/ccga.md)
 * [CCGA_DX](/docs/ccga_dx.md)
 * [CFC](docs/binac.md)

conf/cbe.config

@@ -0,0 +1,32 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'CLIP BATCH ENVIRONMENT (CBE) cluster profile provided by nf-core/configs'
+  config_profile_contact = 'Patrick Hüther (@phue)'
+  config_profile_url = 'http://www.gmi.oeaw.ac.at/'
+}
+
+process {
+  executor = 'slurm'
+  module = 'singularity/3.1.0'
+  queue = 'c'
+}
+
+singularity.enabled = true
+
+params {
+  target_qos = 'medium'
+  params.max_cpus = 36
+  params.max_memory = 170.GB
+  igenomesIgnore = true
+}
+
+if (params.target_qos == 'short') {
+  params.max_time = 8.h
+  process.clusterOptions = '--qos short'
+} else if (params.target_qos == 'medium') {
+  params.max_time = 2.d
+  process.clusterOptions = '--qos medium'
+} else {
+  params.max_time = 14.d
+  process.clusterOptions = '--qos long'
+}

docs/cbe.md

@@ -0,0 +1,18 @@
+# nf-core/configs: CBE Configuration
+
+All nf-core pipelines have been successfully configured for use on the CLIP BATCH ENVIRONMENT (CBE) cluster at the Vienna BioCenter (VBC).
+
+To use, run the pipeline with `-profile cbe`. This will download and launch the [`cbe.config`](../conf/cbe.config) which has been pre-configured with a setup suitable for the CBE 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 CBE. You can do this by issuing the commands below:
+
+```bash
+## Load Nextflow and Singularity environment modules
+module purge
+module load nextflow/19.04.0
+module load singularity/3.1.0
+```
+
+>NB: You will need an account to use the HPC cluster on CBE 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.

nfcore_custom.config

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