Commit d7cb4cb6 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) `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) `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 use a specific [`-profile`](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#mandatory-option) for your cluster.
* Write in a file `Script.sh`:
* Write in a file `Script.sh`:
```python
#!/bin/bash
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**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`
* Run `Script.sh`
```python
sbatch Script.sh
```
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