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correct md to pass linter

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noirot 2019-11-26 14:43:42 +01:00
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@ -10,37 +10,41 @@ Using this profile, a docker image containing all of the required software
will be downloaded, and converted to a Singularity image before execution 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/`. 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. ## Running the workflow ib the Genologin cluster
Before running the pipeline you will need to load Nextflow and Before running the pipeline you will need to load Nextflow and
Singularity using the environment module system on Genotoul. You can do Singularity using the environment module system on Genotoul. You can do
this by issuing the commands below: this by issuing the commands below:
Once connected on our frontal node : Once connected on our frontal node :
```
```bash
# Login to a compute node # Login to a compute node
srun --mem=4G --pty bash srun --mem=4G --pty bash
``` ```
Setup default nextflow and singularity home directory (to be done only one time): Setup default nextflow and singularity home directory (to be done only one time):
```
```bash
sh /usr/local/bioinfo/src/NextflowWorkflows/create_nfx_dirs.sh sh /usr/local/bioinfo/src/NextflowWorkflows/create_nfx_dirs.sh
``` ```
Load environment : Load environment :
```
```bash
module purge module purge
module load bioinfo/nfcore-Nextflow-v19.04.0 module load bioinfo/nfcore-Nextflow-v19.04.0
``` ```
Try a test workflow (for example the methylseq workflow) : Try a test workflow (for example the methylseq workflow) :
```
```bash
nextflow run nf-core/methylseq -profile genotoul,test nextflow run nf-core/methylseq -profile genotoul,test
``` ```
Create launch script `nfcore-rnaseq.sh` : Create launch script `nfcore-rnaseq.sh` :
```
```bash
#!/bin/bash #!/bin/bash
#SBATCH -p workq #SBATCH -p workq
#SBATCH -t 1:00:00 #time in hour #SBATCH -t 1:00:00 #time in hour
@ -51,7 +55,8 @@ module load bioinfo/nfcore-Nextflow-v19.04.0
nextflow run nf-core/methylseq -profile genotoul,test nextflow run nf-core/methylseq -profile genotoul,test
``` ```
Launch on the cluster with sbatch: Launch on the cluster with sbatch:
```
```bash
sbatch nfcore-rnaseq.sh sbatch nfcore-rnaseq.sh
``` ```
@ -64,10 +69,9 @@ By default, available mount points are :
- /work - /work
- /work2 - /work2
To have access to specific other mount point (such as nosave or project) To have access to specific other mount point (such as nosave or project)
you can add a config profile file with option `-profile` and wich contain: you can add a config profile file with option `-profile` and wich contain:
``` ```bash
singularity.runOptions = '-B /diretory/to/mount' singularity.runOptions = '-B /diretory/to/mount'
``` ```
@ -77,6 +81,5 @@ A local copy of several genomes are available in `/bank` directory. See
our [databank page](http://bioinfo.genotoul.fr/index.php/resources-2/databanks/) our [databank page](http://bioinfo.genotoul.fr/index.php/resources-2/databanks/)
to search for your favorite genome. to search for your favorite genome.
>NB: You will need an account to use the HPC cluster on Genotoul in order >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/. to run the pipeline. If in doubt see [http://bioinfo.genotoul.fr/](http://bioinfo.genotoul.fr/).