diff --git a/conf/binac.config b/conf/binac.config index e2bce86..9447ca4 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -13,14 +13,13 @@ process { beforeScript = 'module load devel/singularity/3.0.3' executor = 'pbs' queue = 'short' - process.queue = { task.memory > 128.GB ? 'smp': task.time <= 20m ? 'tiny' : task.time <= 48.h ? 'short' : task.time <= 168.h ? 'long'} } params { igenomes_base = '/nfsmounts/igenomes' - max_memory = 1024.GB + max_memory = 128.GB max_cpus = 28 - max_time = 168.h + max_time = 48.h } weblog{ diff --git a/docs/pasteur.md b/docs/pasteur.md index 6e2d825..554761b 100644 --- a/docs/pasteur.md +++ b/docs/pasteur.md @@ -4,38 +4,36 @@ All nf-core pipelines have been successfully configured for use on the tars clus To use, run the pipeline with `-profile pasteur`. This will download and launch the [`pasteur.config`](../conf/pasteur.config) which has been pre-configured with a setup suitable for the Pasteur 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. + + ## Running the workflow on the Pasteur cluster Nextflow is not installed by default on the Pasteur cluster. - - Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#) + Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command. Nextflow shouldn't run directly on the submission node but on a compute node. The compute nodes don't have access to internet so you need to run it offline. To do that: - 1. Create a virtualenv to install nf-core - - ```bash - module purge - module load Python/3.6.0 - module load java - module load singularity - cd /path/to/nf-core/workflows - virtualenv .venv -p python3 - . .venv/bin/activate - ``` - +```bash +module purge +module load Python/3.6.0 +module load java +module load singularity +cd /path/to/nf-core/workflows +virtualenv .venv -p python3 +. .venv/bin/activate +``` 2. Install nf-core: [here](https://nf-co.re/tools#installation) 3. Get nf-core pipeline and container: [here](https://nf-co.re/tools#downloading-pipelines-for-offline-use) -4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/configs#offline-usage) -5. Run nextflow on a compute node: - +4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/rnaseq/blob/master/docs/usage.md#--custom_config_base) +5. Run nextflow on a compute node: ```bash # create a terminal -tmux +tmux # Get a compute node salloc @@ -48,7 +46,7 @@ module load singularity # Run nextflow workflow nextflow run \\ /path/to/pipeline-dir/from/step/3/workflow \\ --resume +-resume -profile pasteur \\ -with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\ --email my-email@pasteur.fr \\