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Fixed linting in usage.md
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CarsonJM committed Feb 1, 2024
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Expand Up @@ -281,35 +281,35 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio
2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags)
3. Create the custom config accordingly:

- For Docker:

```nextflow
process {
withName: PANGOLIN {
container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0'
}
}
```
- For Singularity:
```nextflow
process {
withName: PANGOLIN {
container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0'
}
}
```
- For Conda:
```nextflow
process {
withName: PANGOLIN {
conda = 'bioconda::pangolin=3.0.5'
}
}
```
- For Docker:

```nextflow
process {
withName: PANGOLIN {
container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0'
}
}
```

- For Singularity:

```nextflow
process {
withName: PANGOLIN {
container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0'
}
}
```

- For Conda:

```nextflow
process {
withName: PANGOLIN {
conda = 'bioconda::pangolin=3.0.5'
}
}
```

> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch.
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