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Merge pull request #158 from phue/singularity_global

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CBE: don't load singularity module
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Phil Ewels 2020-06-05 12:20:39 +02:00 committed by GitHub
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2 changed files with 2 additions and 4 deletions
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1
conf/cbe.config
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@ -7,7 +7,6 @@ params {
process { process {
executor = 'slurm' executor = 'slurm'
module = 'singularity/3.4.1'
queue = { task.memory <= 170.GB ? 'c' : 'm' } queue = { task.memory <= 170.GB ? 'c' : 'm' }
clusterOptions = { task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' } clusterOptions = { task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' }
} }

5
docs/cbe.md
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@ -4,13 +4,12 @@ All nf-core pipelines have been successfully configured for use on the CLIP BATC
To use, run the pipeline with `-profile cbe`. This will download and launch the [`cbe.config`](../conf/cbe.config) which has been pre-configured with a setup suitable for the CBE 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. To use, run the pipeline with `-profile cbe`. This will download and launch the [`cbe.config`](../conf/cbe.config) which has been pre-configured with a setup suitable for the CBE 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.
Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on CBE. You can do this by issuing the commands below: Before running the pipeline you will need to load Nextflow using the environment module system on CBE. You can do this by issuing the commands below:
```bash ```bash
## Load Nextflow and Singularity environment modules ## Load Nextflow environment module
module purge module purge
module load nextflow/19.04.0 module load nextflow/19.04.0
module load singularity/3.2.1
``` ```
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.