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more azurebatch to more appropriate section
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maxulysse committed Sep 2, 2022
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> 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`.
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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If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
## Azure Resource Requests
To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
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).
# Troubleshooting & FAQ
## How to test the pipeline
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