Merge pull request #724 from maxulysse/dev

fix prettier

CHANGELOG.md

@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#696](https://github.com/nf-core/sarek/pull/696) - Adding check of md5-sums in CI-tests
 - [#719](https://github.com/nf-core/sarek/pull/719) - Added boxes to subway map
 - [#720](https://github.com/nf-core/sarek/pull/720) - Sync `TEMPLATE` with `tools` `2.5`
+- [#723](https://github.com/nf-core/sarek/pull/723) - Sync `TEMPLATE` with `tools` `2.5.1`
 
 ### Fixed
 
@@ -30,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#689](https://github.com/nf-core/sarek/pull/689) - Fixed when clause for non `BWA mem` building mapping indexes
 - [#704](https://github.com/nf-core/sarek/pull/704) - Fixed `cf_ploidy` to string instead of number
 - [#706](https://github.com/nf-core/sarek/pull/706) - Fixed `vep_version` not found error when running `--vep_loftee`
+- [#724](https://github.com/nf-core/sarek/pull/724) - Fixed prettier issue
 
 ### Deprecated
 

docs/usage.md

@@ -428,13 +428,6 @@ 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`.
-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`.
@@ -483,6 +476,14 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config
 
 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