mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-23 00:39:56 +00:00
88 lines
2.4 KiB
Markdown
88 lines
2.4 KiB
Markdown
# 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.
|
|
|
|
To use, run the pipeline with `-profile genotoul`. This will download and
|
|
launch the [`genotoul.config`](../conf/genotoul.config) which has been
|
|
pre-configured with a setup suitable for the Bioinfo Genotoul 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. Images are stored for all users in following directory `/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/`.
|
|
|
|
## Running the workflow ib the Genologin cluster
|
|
|
|
Before running the pipeline you will need to load Nextflow and
|
|
Singularity using the environment module system on Genotoul. You can do
|
|
this by issuing the commands below:
|
|
|
|
Once connected on our frontal node :
|
|
|
|
```bash
|
|
# Login to a compute node
|
|
srun --mem=4G --pty bash
|
|
```
|
|
|
|
Setup default nextflow and singularity home directory (to be done only one time):
|
|
|
|
```bash
|
|
sh /usr/local/bioinfo/src/NextflowWorkflows/create_nfx_dirs.sh
|
|
```
|
|
|
|
Load environment :
|
|
|
|
```bash
|
|
module purge
|
|
module load bioinfo/nfcore-Nextflow-v19.04.0
|
|
```
|
|
|
|
Try a test workflow (for example the methylseq workflow) :
|
|
|
|
```bash
|
|
nextflow run nf-core/methylseq -profile genotoul,test
|
|
```
|
|
|
|
Create launch script `nfcore-rnaseq.sh` :
|
|
|
|
```bash
|
|
#!/bin/bash
|
|
#SBATCH -p workq
|
|
#SBATCH -t 1:00:00 #time in hour
|
|
#SBATCH --mem=4G
|
|
#SBATCH --mail-type=BEGIN,END,FAIL
|
|
|
|
module load bioinfo/nfcore-Nextflow-v19.04.0
|
|
nextflow run nf-core/methylseq -profile genotoul,test
|
|
```
|
|
|
|
Launch on the cluster with sbatch:
|
|
|
|
```bash
|
|
sbatch nfcore-rnaseq.sh
|
|
```
|
|
|
|
## Mounted directory
|
|
|
|
By default, available mount points are:
|
|
|
|
* /bank
|
|
* /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:
|
|
|
|
```bash
|
|
singularity.runOptions = '-B /directory/to/mount'
|
|
```
|
|
|
|
## Databanks
|
|
|
|
A local copy of several genomes are available in `/bank` directory. See
|
|
our [databank page](http://bioinfo.genotoul.fr/index.php/resources-2/databanks/)
|
|
to search for your favorite genome.
|
|
|
|
>NB: You will need an account to use the HPC cluster on Genotoul in order
|
|
to run the pipeline. If in doubt see [http://bioinfo.genotoul.fr/](http://bioinfo.genotoul.fr/).
|