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Add in Azure config documentation #716

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Sep 2, 2022
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Add in Azure config documentation #716

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7543e76
Add Azure config recommendations.
vsmalladi Aug 24, 2022
1faeb12
Update CHANGELOG.md
vsmalladi Aug 24, 2022
8a6fde6
Update CHANGELOG.md
vsmalladi Aug 24, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added

- [#691](https://github.com/nf-core/sarek/pull/691) - Enable `PROFILE=conda`, `PROFILE=docker` and `PROFILE=singularity` for pytest
- [#716](https://github.com/nf-core/sarek/pull/716) - Add documentation for Azure recomended config vm_size

### Changed

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7 changes: 7 additions & 0 deletions docs/usage.md
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Expand Up @@ -428,6 +428,13 @@ process {
>
> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly.

## Azure Resource Requests

To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
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We recomend providing a compute `params.vm_type` of `Standard_E64_v3` VMs by default but these options can be changed if required.

Note that the choice of VM size depends on your quota and the overall workload during the analysis.For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes).

## Updating containers

The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`.
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