Merge pull request #827 from CodingKaiser/master

Updated FGCZ configuration

conf/fgcz.config

@@ -1,6 +1,6 @@
 params {
     config_profile_description = "FGCZ ETH/UZH"
-    config_profile_contact     = "natalia.zajac@fgcz.ethz.ch"
+    config_profile_contact     = "falnoe@ethz.ch"
     max_memory                 = 500.GB
     max_cpus                   = 64
     max_time                   = 240.h
@@ -17,13 +17,11 @@ process {
 }
 
 executor {
-    queueSize = 30
+    queueSize = 10
 }
 
-
-
-singularity {
+apptainer {
     enabled    = true
     autoMounts = true
-    cacheDir   = "/srv/GT/nextflow/singularity/"
+    cacheDir   = "/srv/GT/software/apptainer/cache"
 }

docs/fgcz.md

@@ -2,17 +2,21 @@
 
 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.
+Note that, at present, this config has only been tested with `nf-core/viralrecon` and `nf-core/atacseq`, 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 the singularity cache in your /srv/GT/ directory for access by all projects.
+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 an apptainer image before execution of the pipeline. **This requires a local installation of apptainer**. 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 the apptainer cache in your `/srv/GT/software/apptainer/cache` directory for access by all projects.
 
-Example: /usr/local/ngseq/src/nextflow/nextflow run -profile fgcz
+For example:
+
+```shell
+nextflow run -profile fgcz ...
+```
 
 ## Before running the pipeline
 
-Load the following modules before running any nf-core pipelines.
+You may need to load the jdk module before running any nextflow pipelines.
 
-```bash
-module load Dev/Python/3.8.3
+```shell
+module load Dev/jdk/21
 ```