Merge pull request #341 from zajacn/master

Addition of FGCZ config

.github/workflows/main.yml

@@ -39,6 +39,7 @@ jobs:
             - 'ebc'
             - 'eddie'
             - 'eva'
+            - 'fgcz'
             - 'genotoul'
             - 'genouest'
             - 'gis'

README.md

@@ -107,6 +107,7 @@ Currently documentation is available for the following systems:
 * [DENBI_QBIC](docs/denbi_qbic.md)
 * [EBC](docs/ebc.md)
 * [EVA](docs/eva.md)
+* [FGCZ](docs/fgcz.md)
 * [GENOTOUL](docs/genotoul.md)
 * [GENOUEST](docs/genouest.md)
 * [GIS](docs/gis.md)

conf/fgcz.config

@@ -0,0 +1,24 @@
+params {
+	config_profile_description = "FGCZ ETH/UZH"
+	config_profile_contact = "natalia.zajac@fgcz.ethz.ch"
+	max_memory = 500.GB
+	max_cpus = 64
+	max_time = 240.h
+}
+
+process {
+	executor = "slurm"
+	maxRetries = 2
+}
+
+executor {
+	queueSize = 30
+}
+
+
+
+singularity {
+	enabled = true
+	autoMounts = true
+	cacheDir = "/srv/GT/nextflow/singularity/"
+}

docs/fgcz.md

@@ -0,0 +1,18 @@
+# nf-core/configs: FGCZ Configuration
+
+Configuration file to run nf-core pipelines on the cluster of the [Functional Genomics Center Zurich](https://fgcz.ch/), a research and training facility of the ETH Zürich and the University of Zurich.
+
+Note that, at present, this config has only been tested with nf-core/viralrecon, but should function similarly for other nf-core pipelines.
+
+To use, run the pipeline with `-profile fgcz`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the FGCZ 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. **This requires a local installation of singularity**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node.
+The config places your singularity cashe in your home directory for access by other projects your run in other working directories.
+
+Example: /usr/local/ngseq/src/nextflow/nextflow run -profile fgcz
+
+## Before running the pipeline
+
+Load the following modules before running any nf-core pipelines.
+
+```bash
+module load Dev/Python/3.8.3
+```

nfcore_custom.config

@@ -33,6 +33,7 @@ profiles {
   ebc          { includeConfig "${params.custom_config_base}/conf/ebc.config" }
   eddie        { includeConfig "${params.custom_config_base}/conf/eddie.config" }
   eva          { includeConfig "${params.custom_config_base}/conf/eva.config" }
+  fgcz         { includeConfig "${params.custom_config_base}/conf/fgcz.config" }
   genotoul     { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
   genouest     { includeConfig "${params.custom_config_base}/conf/genouest.config" }
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }