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Merge pull request nf-core#692 from noirot/master
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Update genotoul documentation
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maxulysse authored May 22, 2024
2 parents 8eeb9eb + d15bd47 commit aeecb3b
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14 changes: 6 additions & 8 deletions docs/genotoul.md
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# nf-core/configs: Bioinfo Genotoul Configuration

All nf-core pipelines have been successfully configured for use on the Bioinfo Genotoul cluster at the INRA toulouse.
All nf-core pipelines have been successfully configured for use on the Bioinfo Genotoul cluster at the INRAe toulouse.

To use, run the pipeline with `-profile genotoul`. This will download and
launch the [`genotoul.config`](../conf/genotoul.config) which has been
Expand Down Expand Up @@ -33,7 +33,7 @@ Load environment :

```bash
module purge
module load bioinfo/nfcore-Nextflow-v19.04.0
module load bioinfo/NextflowWorkflows/nfcore-Nextflow-v23.10.0
```

Try a test workflow (for example the methylseq workflow) :
Expand All @@ -42,7 +42,7 @@ Try a test workflow (for example the methylseq workflow) :
nextflow run nf-core/methylseq -profile genotoul,test
```

Create launch script `nfcore-rnaseq.sh` :
Create launch script `nfcore-methylseq.sh` :

```bash
#!/bin/bash
Expand All @@ -51,14 +51,14 @@ Create launch script `nfcore-rnaseq.sh` :
#SBATCH --mem=4G
#SBATCH --mail-type=BEGIN,END,FAIL

module load bioinfo/nfcore-Nextflow-v19.04.0
module load bioinfo/NextflowWorkflows/nfcore-Nextflow-v23.10.0
nextflow run nf-core/methylseq -profile genotoul,test
```

Launch on the cluster with sbatch:

```bash
sbatch nfcore-rnaseq.sh
sbatch nfcore-methylseq.sh
```

## Mounted directory
Expand All @@ -69,10 +69,8 @@ By default, available mount points are:
- /home
- /save
- /work
- /work2

To have access to specific other mount point (such as nosave or project)
you can add a config profile file with option `-profile` and which contain:
To have access to specific other mount point you can add a config profile file with option `-profile` and which contain:

```bash
singularity.runOptions = '-B /directory/to/mount'
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