Ethz euler

.github/workflows/main.yml

@@ -61,6 +61,7 @@ jobs:
           - "ebi_codon_slurm"
           - "eddie"
           - "engaging"
+          - "ethz_euler"
           - "eva"
           - "fgcz"
           - "fub_curta"

README.md

@@ -118,6 +118,7 @@ Currently documentation is available for the following systems:
 - [EBI_CODON](docs/ebi_codon.md)
 - [EBI_CODON_SLURM](docs/ebi_codon_slurm.md)
 - [Engaging](docs/engaging.md)
+- [ETH Zurich Euler](docs/ethz_euler.md)
 - [EVA](docs/eva.md)
 - [FGCZ](docs/fgcz.md)
 - [FUB Curta](docs/fub_curta.md)

conf/ethz_euler.config

@@ -0,0 +1,49 @@
+/*
+* ------------------------------------------------------------------
+*   nf-core pipelines config file for the ETH Zurich Euler cluster
+* ------------------------------------------------------------------
+*/
+
+params {
+        config_profile_name        = 'ethz_euler'
+        config_profile_description = 'ETH Zurich Euler cluster profile -- provided by nf-core/configs'
+        config_profile_contact     = 'Joao Agostinho de Sousa (github: @jpadesousa; email: [email protected])'
+        config_profile_url         = 'https://scicomp.ethz.ch/wiki/Euler'
+
+        max_memory = 4.TB
+        max_cpus   = 128
+        max_time   = 120.h
+
+	igenomes_base   = '/cluster/project/igenomes'
+        igenomes_ignore = false
+}
+
+executor {
+        name                = 'slurm'
+        perCpuMemAllocation = true
+}
+
+process {
+        scratch             = 'true'
+        errorStrategy       = 'retry'
+        maxRetries          = 3
+        beforeScript        = 'module load eth_proxy'
+}
+
+singularity {
+        enabled    = true
+        autoMounts = true
+}
+
+trace {
+        trace.overwrite = true
+        enabled         = true
+}
+
+// On a successful completion of a Nextflow run, automatically delete all intermediate files stored in the work/ directory
+cleanup = true
+
+// Allows to override the default cleanup = true behaviour for debugging
+debug {
+  cleanup = false
+}

docs/ethz_euler.md

@@ -0,0 +1,35 @@
+# nf-core/configs: ETH Zurich Euler cluster configuration
+
+Configuration file to run nf-core pipelines on the Euler cluster of [ETH Zurich](https://ethz.ch/).
+
+To use the ETH Zurich Euler cluster configuration, run the pipeline with `-profile ethz_euler`. This will download and launch the [`ethz_euler.config`](../conf/ethz_euler.config), which has been pre-configured with a setup suitable for the Euler cluster. Using this profile, a docker image containing all of the required software will be downloaded and converted to a Singularity container before the execution of the pipeline.
+
+## Before running the pipeline
+
+Currently, Nextflow is not installed by default on the Euler cluster. You have to install Nextflow version **>= 23.07.0-edge** on your custom modules.
+
+> **Important:** Previous Nextflow versions will fail to run the job, since the executor option '**perCpuMemAllocation**' is only available since **23.07.0-edge**. This option specifies memory allocations for SLURM jobs as --mem-per-cpu <task.memory / task.cpus> instead of --mem <task.memory>.
+
+
+To run Nextflow on Euler, you will need to load the following modules:
+
+```openjdk``` - a free and opensource java implementation; <br />
+```eth_proxy``` - for the compute nodes communicate with the Internet through the ETH Zurich proxy server;<br />
+```nextflow``` - enables scalable and reproducible scientific workflows using software containers *(this module can have a user-defined name since was a custom installation)*.
+
+```bash
+module load openjdk eth_proxy nextflow
+```
+
+Finally, you will also need to specify the Singularity cache directory with the environmental variable ```APPTAINER_CACHEDIR```.
+
+## Genomes
+In ```/cluster/project/igenomes```, the Euler cluster provides a set of reference genomes and annotations (illumina igenomes) for a selection of model organism. The genomes and annotations were downloaded from: https://support.illumina.com/sequencing/sequencing_software/igenome.html 
+
+The path for the *igenomes* saved in the Euler cluster is already assigned to the parameter variable ```igenomes_base``` and the parameter variable ```igenomes_ignore``` is set to ```false``` so that it loads the igenomes.config when running the pipeline. These default values can be overwritten when running the Nextflow command.
+```
+igenomes_base   = '/cluster/project/igenomes'
+igenomes_ignore = false
+```
+
+*(For more information : https://scicomp.ethz.ch/wiki/Reference_genomes)*

nfcore_custom.config

@@ -43,6 +43,7 @@ profiles {
     ebi_codon        { includeConfig "${params.custom_config_base}/conf/ebi_codon.config" }
     ebi_codon_slurm  { includeConfig "${params.custom_config_base}/conf/ebi_codon_slurm.config" }
     engaging         { includeConfig "${params.custom_config_base}/conf/engaging.config" }
+    ethz_euler       { includeConfig "${params.custom_config_base}/conf/ethz_euler.config" }
     eva              { includeConfig "${params.custom_config_base}/conf/eva.config" }
     fgcz             { includeConfig "${params.custom_config_base}/conf/fgcz.config" }
     fub_curta        { includeConfig "${params.custom_config_base}/conf/fub_curta.config" }