mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-13 05:03:10 +00:00
CBE: don't load singularity module
singularity is now installed from CentOS repos, the environment module will be removed
This commit is contained in:
parent
adf90f3994
commit
6d356cc918
2 changed files with 2 additions and 4 deletions
|
@ -7,7 +7,6 @@ params {
|
|||
|
||||
process {
|
||||
executor = 'slurm'
|
||||
module = 'singularity/3.4.1'
|
||||
queue = { task.memory <= 170.GB ? 'c' : 'm' }
|
||||
clusterOptions = { task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' }
|
||||
}
|
||||
|
|
|
@ -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.
|
||||
|
||||
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
|
||||
## Load Nextflow and Singularity environment modules
|
||||
## Load Nextflow environment module
|
||||
module purge
|
||||
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.
|
||||
|
|
Loading…
Reference in a new issue