Commit 9b5bb2f6 authored by Joanna Fourquet's avatar Joanna Fourquet
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Update usage.md

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3. Run a basic script:
The next script is a script working on **genologin slurm cluster**. Il allows to run the default [step](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/README.md#metagwgs-steps) `01_clean_qc` of the pipeline (without host reads deletion and taxonomic affiliation of reads).
> The next script is a script working on **genologin slurm cluster**. Il allows to run the default [step](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/README.md#metagwgs-steps) `01_clean_qc` of the pipeline (without host reads deletion and taxonomic affiliation of reads).
**WARNING:** You must adapt it if you want to run it into your cluster. You must install/load Nextflow and Singularity, and define a specific configuration for your cluster.
* Write in a file `Script.sh`:
```bash
#!/bin/bash
#SBATCH -p workq
#SBATCH --mem=6G
module purge
module load bioinfo/Nextflow-v20.01.0
module load system/singularity-3.5.3
nextflow run -profile test_genotoul_workq metagwgs/main.nf --reads "metagwgs/test/*_{R1,R2}.fastq.gz" --skip_removal_host --skip_kaiju
```
**NOTE:** you can change Nextflow and Singularity versions with other versions available on the cluster (see all versions with `search_module ToolName`). Nextflow version must be >= v20 and Singularity version must be >= v3.
> ```bash
> #!/bin/bash
> #SBATCH -p workq
> #SBATCH --mem=6G
> module purge
> module load bioinfo/Nextflow-v20.01.0
> module load system/singularity-3.5.3
> nextflow run -profile test_genotoul_workq metagwgs/main.nf --reads "metagwgs/test/*_{R1,R2}.fastq.gz" --skip_removal_host --skip_kaiju
> ```
> **NOTE:** you can change Nextflow and Singularity versions with other versions available on the cluster (see all versions with `search_module ToolName`). Nextflow version must be >= v20 and Singularity version must be >= v3.
* Run `Script.sh` with this command line:
```bash
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