update docs

CHANGELOG.md

@@ -20,4 +20,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## 1.2.1 - [2024-07-04]
 
 ### Fixed
-- Fix pipeline not working when protocol is setting to `new`.
+- Fix an issue where the pipeline do not work when `--protocol` is set to `new`.

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/singleron-RD/scrna/releases/tag/1.2.1" target="_blank">singleron-RD/scrna/1.2.0</a>
+  This report has been generated by the <a href="https://github.com/singleron-RD/scrna/releases/tag/1.2.1" target="_blank">singleron-RD/scrna/1.2.1/</a>
   analysis pipeline.
 report_section_order:
   "singleron-RD-scrna-methods-description":

docs/usage.md

@@ -125,6 +125,9 @@ Run the following command to test
 nextflow run singleron-RD/scrna -profile test,docker --outdir results
 ```
 
+> [!NOTE]
+> This command might fail if you have [trouble connecting to raw.githubusercontent.com](https://github.com/openvinotoolkit/openvino/issues/8492).
+
 ### Updating the pipeline
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
@@ -219,34 +222,6 @@ Whilst the default requirements set within the pipeline will hopefully work for
 
 To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
 
-### Custom Containers
-
-In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date.
-
-To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
-
-### Custom Tool Arguments
-
-A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default.
-
-To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website.
-
-### nf-core/configs
-
-In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-core pipelines regularly and need to use the same settings regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter. You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.
-
-See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information about creating your own configuration files.
-
-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 recommend providing a compute `params.vm_type` of `Standard_D16_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).
-
 ## Nextflow memory requirements
 
 In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.