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1
.github/workflows/main.yml
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1
.github/workflows/main.yml
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@ -62,6 +62,7 @@ jobs:
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- 'sanger'
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- 'seg_globe'
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- 'uct_hpc'
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- 'unibe_ibu'
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- 'uppmax'
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- 'utd_ganymede'
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- 'utd_sysbio'
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@ -125,6 +125,7 @@ Currently documentation is available for the following systems:
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* [SANGER](docs/sanger.md)
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* [SEG_GLOBE](docs/seg_globe.md)
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* [UCT_HPC](docs/uct_hpc.md)
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* [UNIBE_IBU](docs/unibe_ibu.md)
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* [UPPMAX](docs/uppmax.md)
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* [UTD_GANYMEDE](docs/utd_ganymede.md)
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* [UTD_SYSBIO](docs/utd_sysbio.md)
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23
conf/unibe_ibu.config
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23
conf/unibe_ibu.config
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params {
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config_profile_description = "University of Bern, Interfaculty Bioinformatics Unit cluster profile"
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config_profile_contact = "irene.keller@dbmr.unibe.ch; info@bioinformatics.unibe.ch"
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config_profile_url = "https://www.bioinformatics.unibe.ch/"
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max_memory = 500.GB
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max_cpus = 128
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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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beforeScript = 'mkdir -p ./tmp/ && export TMPDIR=./tmp/'
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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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}
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5
docs/unibe_ibu.md
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5
docs/unibe_ibu.md
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@ -0,0 +1,5 @@
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# nf-core/configs: UNIBE_IBU Configuration
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Configuration file to run nf-core pipelines on the cluster of the [Interfaculty Bioinformatics Unit](https://www.bioinformatics.unibe.ch/) of the University of Bern.
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To use, run the pipeline with `-profile unibe_ibu`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the IBU 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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@ -56,6 +56,7 @@ profiles {
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sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"}
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seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
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uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
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unibe_ibu { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" }
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uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
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utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
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utd_sysbio { includeConfig "${params.custom_config_base}/conf/utd_sysbio.config" }
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