Merge pull request #271 from theoportlock/master

Adds Rosalind config for KCL!

.github/workflows/main.yml

@@ -54,6 +54,7 @@ jobs:
             - 'pasteur'
             - 'phoenix'
             - 'prince'
+            - 'rosalind'
             - 'sanger'
             - 'seg_globe'
             - 'uct_hpc'

README.md

@@ -123,6 +123,7 @@ Currently documentation is available for the following systems:
 * [PASTEUR](docs/pasteur.md)
 * [PHOENIX](docs/phoenix.md)
 * [PRINCE](docs/prince.md)
+* [ROSALIND](docs/rosalind.md)
 * [SANGER](docs/sanger.md)
 * [SEG_GLOBE](docs/seg_globe.md)
 * [UCT_HPC](docs/uct_hpc.md)

conf/rosalind.config

@@ -0,0 +1,29 @@
+params {
+  config_profile_description = 'Kings College London Rosalind HPC'
+  config_profile_contact = 'Theo Portlock'
+  config_profile_url = 'https://www.rosalind.kcl.ac.uk/'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  docker.enabled = false
+}
+
+params {
+  max_memory = 64.GB
+  max_cpus = 16
+  max_time = 24.h
+  partition = 'shared'
+  schema_ignore_params = 'partition,genomes,modules'
+}
+
+process {
+  executor = 'slurm'
+  maxRetries = 3
+  clusterOptions = { "--partition=$params.partition" }
+}
+
+executor {
+  submitRateLimit = '1 sec'
+}

docs/cambridge.md

@@ -1,7 +1,7 @@
 # nf-core/configs: Cambridge HPC Configuration
 
 All nf-core pipelines have been successfully configured for use on the Cambridge HPC cluster at the [The University of Cambridge](https://www.cam.ac.uk/).  
-To use, run the pipeline with `-profile cambridge`. This will download and launch the [`cambridge.config`](../conf/cambridge.config) whichhas been pre-configured
+To use, run the pipeline with `-profile cambridge`. This will download and launch the [`cambridge.config`](../conf/cambridge.config) which has been pre-configured
 with a setup suitable for the Cambridge HPC cluster. Using this profile, either a docker image containing all of the required software will be downloaded,
 and converted to a Singularity image or a Singularity image downloaded directly before execution of the pipeline.  
 

docs/rosalind.md

@@ -0,0 +1,25 @@
+# nf-core/configs: Rosalind Configuration
+
+All nf-core pipelines have been successfully configured for use on the Rosalind CLuster at [Kings College London](https://rosalind.kcl.ac.uk/).
+To use, run the pipeline with `-profile rosalind`. This will download and launch the [`rosalind.config`](../conf/rosalind.config) which has been pre-configured with a setup suitable for the rosalind 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.
+
+## Using Nextflow on Rosalind
+
+Before running the pipeline you will need to configure Nextflow and Singularity. There is no Nextflow module on Rosalind at this time. This can be done with the following commands:
+
+```bash
+## Load Singularity environment modules - these commands can be placed in your ~/.bashrc also
+module load apps/openjdk
+module load apps/singularity
+
+## Download Nextflow-all
+wget https://github.com/nextflow-io/nextflow/releases/download/v21.04.3/nextflow-21.04.3-all
+chmod a+x nextflow-21.04.3-all
+mv nextflow-21.04.3-all ~/bin/nextflow
+```
+
+By default, the shared partition is used for job submission. Other partitions can be specified using the `--partition <PARTITION NAME>` argument to the run.
+
+## Additional information
+
+The default shared partition resource limits are defined as ten percent of the total available to the cluster at any one point in time. The limitations defined by this configuration are conservative and are projected to be increased as greater computational resources are introduced in the near future.

nfcore_custom.config

@@ -48,6 +48,7 @@ profiles {
   pasteur      { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
   phoenix      { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
   prince       { includeConfig "${params.custom_config_base}/conf/prince.config" }
+  rosalind     { includeConfig "${params.custom_config_base}/conf/rosalind.config" }
   sanger       { includeConfig "${params.custom_config_base}/conf/sanger.config"}
   seg_globe    { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
   uct_hpc      { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }