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Config Addition
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.github/workflows/main.yml
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.github/workflows/main.yml
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@ -39,6 +39,7 @@ jobs:
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- 'ebc'
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- 'eddie'
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- 'eva'
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- 'fgcz'
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- 'genotoul'
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- 'genouest'
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- 'gis'
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@ -107,6 +107,7 @@ Currently documentation is available for the following systems:
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* [DENBI_QBIC](docs/denbi_qbic.md)
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* [EBC](docs/ebc.md)
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* [EVA](docs/eva.md)
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* [FGCZ](docs/fgcz.md)
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* [GENOTOUL](docs/genotoul.md)
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* [GENOUEST](docs/genouest.md)
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* [GIS](docs/gis.md)
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24
conf/fgcz.config
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conf/fgcz.config
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params {
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config_profile_description = "FGCZ ETH/UZH"
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config_profile_contact = "natalia.zajac@fgcz.ethz.ch"
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max_memory = 500.GB
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max_cpus = 64
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max_time = 240.h
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}
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process {
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executor = "slurm"
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maxRetries = 2
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}
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executor {
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queueSize = 30
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}
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singularity {
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enabled = true
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autoMounts = true
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cacheDir = "/home/$USER/singularity/"
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}
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18
docs/fgcz.md
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docs/fgcz.md
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# nf-core/configs: FGCZ Configuration
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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.
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Note that, at present, this config has only been tested with nf-core/viralrecon, but should function similarly for other nf-core pipelines.
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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.
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The config places your singularity cashe in your home directory for access by other projects your run in other working directories.
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Example: /usr/local/ngseq/src/nextflow/nextflow run -profile fgcz
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## Before running the pipeline
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Load the following modules before running any nf-core pipelines.
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```bash
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module load Dev/Python/3.8.3
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```
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@ -33,6 +33,7 @@ profiles {
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ebc { includeConfig "${params.custom_config_base}/conf/ebc.config" }
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eddie { includeConfig "${params.custom_config_base}/conf/eddie.config" }
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eva { includeConfig "${params.custom_config_base}/conf/eva.config" }
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fgcz { includeConfig "${params.custom_config_base}/conf/fgcz.config" }
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genotoul { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
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genouest { includeConfig "${params.custom_config_base}/conf/genouest.config" }
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gis { includeConfig "${params.custom_config_base}/conf/gis.config" }
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