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Merge pull request #320 from rbpisupati/cbe-singularity

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cbe: update config and docs
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Patrick Hüther 2022-02-04 10:40:16 +01:00 committed by GitHub
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2 changed files with 4 additions and 6 deletions
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8
conf/cbe.config
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@ -7,11 +7,9 @@ params {
process { process {
executor = 'slurm' executor = 'slurm'
queue = { task.memory <= 170.GB ? 'c' : 'm' } queue = { task.memory <= 120.GB ? 'c' : 'm' }
module = 'anaconda3/2019.10' module = ['build-env/.f2021', 'build-env/f2021', 'anaconda3/2021.11']
clusterOptions = { ( task.queue == 'g' ? '--gres gpu:1 ' : '' ) << ( (task.queue == 'c' & task.time <= 1.h) ? '--qos rapid' : ( task.time <= 8.h ? '--qos short': ( task.time <= 48.h ? '--qos medium' : '--qos long' ) ) ) }
// --signal option will be handled by nextflow after 21.10.0 release (see https://github.com/nextflow-io/nextflow/issues/2163)
clusterOptions = { '--signal B:USR2 ' << ( (queue == 'c' & task.time <= 1.h) ? '--qos rapid' : ( task.time <= 8.h ? '--qos short': ( task.time <= 48.h ? '--qos medium' : '--qos long' ) ) ) }
} }
singularity { singularity {

2
docs/cbe.md
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@ -9,7 +9,7 @@ Before running the pipeline you will need to load Nextflow using the environment
```bash ```bash
## Load Nextflow environment module ## Load Nextflow environment module
module purge module purge
module load nextflow/19.04.0 module load nextflow/21.10.6
``` ```
A local copy of the [AWS-iGenomes](https://registry.opendata.aws/aws-igenomes/) resource has been made available on CBE so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome <GENOME_ID>` parameter. A local copy of the [AWS-iGenomes](https://registry.opendata.aws/aws-igenomes/) resource has been made available on CBE so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome <GENOME_ID>` parameter.