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80 lines
2.3 KiB
Markdown
80 lines
2.3 KiB
Markdown
# nf-core/configs: ABiMS Configuration
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All nf-core pipelines have been successfully configured for use on the ABiMS cluster.
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To use, run the pipeline with `-profile abims`. This will download and launch the [`abims.config`](../conf/abims.config) which has been pre-configured with a setup suitable for the ABiMS 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.
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## Request an account
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You will need an account to use the HPC cluster on ABiMS in order
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to run the pipeline. If in doubt see [http://abims.sb-roscoff.fr/account](http://abims.sb-roscoff.fr/account).
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## Running the workflow on the ABiMS cluster
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Nextflow is installed on the ABiMS cluster.
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You need to activate it like this:
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```bash
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module load nextflow slurm-drmaa graphviz
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```
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Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command.
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Nextflow shouldn't run directly on the submission node but on a compute node. Run nextflow from a compute node:
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```bash
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# Load the dependencies if not done before
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module load nextflow slurm-drmaa graphviz
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# Run a downloaded/git-cloned nextflow workflow from
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srun nextflow run \
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/path/to/nf-core/workflow \
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-profile abims \
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--email my-email@example.org \
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-c my-specific.config
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...
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# Or use let nf-core client download the workflow
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srun nextflow run nf-core/rnaseq -profile abims ...
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# To launch in background
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sbatch --wrap "nextflow run nf-core/rnaseq -profile abims ..."
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```
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Or write a sbatch script
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> nfcore-rnaseq.sh
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```bash
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#!/bin/bash
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#SBATCH -p fast
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#SBATCH --mem=4G
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module load nextflow slurm-drmaa graphviz
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nextflow run nf-core/rnaseq -profile abims ...
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```
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Launch on the cluster with sbatch:
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```bash
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sbatch nfcore-rnaseq.sh
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```
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### Hello, world
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nf-core provides some test for each workflow:
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```bash
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module load nextflow slurm-drmaa graphviz
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nextflow run nf-core/rnaseq -profile abims,test
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```
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## Singularity images mutualized directory
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To reduce the disk usage, nf-core images can be stored in a mutualized directory: `/shared/software/singularity/images/nf-core/`
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The environment variable `NXF_SINGULARITY_CACHEDIR: /shared/data/cache/nextflow` will indicate this directory to nextflow.
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## Databanks
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A local copy of several genomes are available in `/shared/bank/` directory.
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