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54 lines
1.9 KiB
Markdown
54 lines
1.9 KiB
Markdown
# nf-core/configs: Wellcome Sanger Institute Configuration
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To use, run the pipeline with `-profile sanger`. This will download and launch the [`sanger.config`](../conf/sanger.config) which has been
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pre-configured with a setup suitable for the Wellcome Sanger Institute LSF cluster.
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## Running the workflow on the Wellcome Sanger Institute cluster
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The latest version of Nextflow is not installed by default on the cluster. You will need to install it into a directory you have write access to
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- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
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A recommended place to move the `nextflow` executable to is `~/bin` so that it's in the `PATH`.
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Nextflow manages each process as a separate job that is submitted to the cluster by using the `bsub` command.
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If asking Nextflow to use Singularity to run the individual jobs,
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you should make sure that your account has access to the Singularity binary by adding these lines to your `.bashrc` file
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```bash
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[[ -f /software/modules/ISG/singularity ]] && module load ISG/singularity
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```
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Nextflow shouldn't run directly on the submission node but on a compute node.
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To do so make a shell script with a similar structure to the following code and submit with `bsub < $PWD/my_script.sh`
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```bash
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#!/bin/bash
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#BSUB -o /path/to/a/log/dir/%J.o
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#BSUB -e /path/to/a/log/dir/%J.e
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#BSUB -M 8000
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#BSUB -q oversubscribed
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#BSUB -n 2
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export HTTP_PROXY='http://wwwcache.sanger.ac.uk:3128'
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export HTTPS_PROXY='http://wwwcache.sanger.ac.uk:3128'
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export NXF_ANSI_LOG=false
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export NXF_OPTS="-Xms8G -Xmx8G -Dnxf.pool.maxThreads=2000"
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export NXF_VER=22.04.0-5697
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nextflow run \
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/path/to/nf-core/pipeline/main.nf \
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-w /path/to/some/dir/work \
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-profile sanger \
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-c my_specific.config \
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-qs 1000 \
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-resume
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## clean up on exit 0 - delete this if you want to keep the work dir
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status=$?
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if [[ $status -eq 0 ]]; then
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rm -r /path/to/some/dir/work
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fi
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```
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