From 6b780bf2f60e84c7a8228805ad90cabcfe365f92 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 8 Aug 2023 15:07:28 +0200
Subject: [PATCH 1/2] update template blockquotes to new admonition styles

---
 README.md                                | 12 ++++++++----
 nf_core/pipeline-template/README.md      | 18 ++++++++++--------
 nf_core/pipeline-template/docs/output.md |  4 +++-
 nf_core/pipeline-template/docs/usage.md  |  4 +++-
 4 files changed, 24 insertions(+), 14 deletions(-)

diff --git a/README.md b/README.md
index 94e452823..6e85fc0f3 100644
--- a/README.md
+++ b/README.md
@@ -227,10 +227,14 @@ Auto-completion for the `nf-core` command is available for bash, zsh and fish. T
 
 After a restart of the shell session you should have auto-completion for the `nf-core` command and all its sub-commands and options.
 
-> **NB:** The added line will run the command `nf-core` (which will also slow down startup time of your shell). You should therefore either have the nf-core/tools installed globally.
-> You can also wrap it inside `if type nf-core > /dev/null; then ` \<YOUR EVAL CODE LINE\> `fi` for bash and zsh or `if command -v nf-core &> /dev/null eval (env _NF_CORE_COMPLETE=fish_source nf-core) end` for fish. You need to then source the config in your environment for the completions to be activated.
-
-> **NB:** If you see the error `command not found compdef` , be sure that your config file contains the line `autoload -Uz compinit && compinit` before the eval line.
+:::note
+The added line will run the command `nf-core` (which will also slow down startup time of your shell). You should therefore either have the nf-core/tools installed globally.
+You can also wrap it inside `if type nf-core > /dev/null; then ` \<YOUR EVAL CODE LINE\> `fi` for bash and zsh or `if command -v nf-core &> /dev/null eval (env _NF_CORE_COMPLETE=fish_source nf-core) end` for fish. You need to then source the config in your environment for the completions to be activated.
+:::
+
+:::info
+If you see the error `command not found compdef` , be sure that your config file contains the line `autoload -Uz compinit && compinit` before the eval line.
+:::
 
 ## Listing pipelines
 
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index e66746dcd..27e96de7f 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -43,10 +43,11 @@
 
 ## Usage
 
-> **Note**
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
-> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
-> with `-profile test` before running the workflow on actual data.
+:::note
+If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
+to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
+with `-profile test` before running the workflow on actual data.
+:::
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -75,10 +76,11 @@ nextflow run {{ name }} \
    --outdir <OUTDIR>
 ```
 
-> **Warning:**
-> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
-> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+:::warning
+Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
+provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
+see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+:::
 
 {% if branded -%}
 
diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md
index 09eb6839d..8a8f48622 100644
--- a/nf_core/pipeline-template/docs/output.md
+++ b/nf_core/pipeline-template/docs/output.md
@@ -35,7 +35,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 ![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
 
-> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+:::note
+The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+:::
 
 ### MultiQC
 
diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md
index e89c2a733..6342823b1 100644
--- a/nf_core/pipeline-template/docs/usage.md
+++ b/nf_core/pipeline-template/docs/usage.md
@@ -120,7 +120,9 @@ To further assist in reproducbility, you can use share and re-use [parameter fil
 
 ## Core Nextflow arguments
 
-> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
+:::note
+These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
+:::
 
 ### `-profile`
 

From 05dc14261640366fb1c87ee2b503cab0ecfcdbdb Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 8 Aug 2023 15:13:49 +0200
Subject: [PATCH 2/2] even more admonitions

---
 README.md                                     | 30 ++++++++++++++-----
 .../pipeline-template/.github/CONTRIBUTING.md |  4 ++-
 nf_core/pipeline-template/docs/usage.md       | 12 ++++++--
 3 files changed, 34 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 6e85fc0f3..5b6908dff 100644
--- a/README.md
+++ b/README.md
@@ -365,14 +365,18 @@ You can run the pipeline by simply providing the directory path for the `workflo
 nextflow run /path/to/download/nf-core-rnaseq-dev/workflow/ --input mydata.csv --outdir results  # usual parameters here
 ```
 
-> Note that if you downloaded Singularity container images, you will need to use `-profile singularity` or have it enabled in your config file.
+:::note
+If you downloaded Singularity container images, you will need to use `-profile singularity` or have it enabled in your config file.
+:::
 
 ### Downloaded nf-core configs
 
 The pipeline files are automatically updated (`params.custom_config_base` is set to `../configs`), so that the local copy of institutional configs are available when running the pipeline.
 So using `-profile <NAME>` should work if available within [nf-core/configs](https://github.com/nf-core/configs).
 
-> ⚠️ This option is not available when downloading a pipeline for use with [Nextflow Tower](#adapting-downloads-to-nextflow-tower) because the application manages all configurations separately.
+:::warning
+This option is not available when downloading a pipeline for use with [Nextflow Tower](#adapting-downloads-to-nextflow-tower) because the application manages all configurations separately.
+:::
 
 ### Downloading Apptainer containers
 
@@ -430,14 +434,18 @@ If the download speeds are much slower than your internet connection is capable
 
 Subsequently, the `*.git` folder can be moved to it's final destination and linked with a pipeline in _Tower_ using the `file:/` prefix.
 
-> 💡 Also without access to Tower, pipelines downloaded with the `--tower` flag can be run: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
+:::tip
+Also without access to Tower, pipelines downloaded with the `--tower` flag can be run: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
+:::
 
 ## Pipeline software licences
 
 Sometimes it's useful to see the software licences of the tools used in a pipeline.
 You can use the `licences` subcommand to fetch and print the software licence from each conda / PyPI package used in an nf-core pipeline.
 
-> ⚠️ This command does not currently work for newer DSL2 pipelines. This will hopefully be addressed [soon](https://github.com/nf-core/tools/issues/1155).
+:::warning
+This command does not currently work for newer DSL2 pipelines. This will hopefully be addressed [soon](https://github.com/nf-core/tools/issues/1155).
+:::
 
 <!-- RICH-CODEX
 timeout: 10
@@ -465,8 +473,10 @@ You can then continue to edit, commit and push normally as you build your pipeli
 
 Please see the [nf-core documentation](https://nf-co.re/developers/adding_pipelines) for a full walkthrough of how to create a new nf-core workflow.
 
-> As the log output says, remember to come and discuss your idea for a pipeline as early as possible!
-> See the [documentation](https://nf-co.re/developers/adding_pipelines#join-the-community) for instructions.
+:::tip
+As the log output says, remember to come and discuss your idea for a pipeline as early as possible!
+See the [documentation](https://nf-co.re/developers/adding_pipelines#join-the-community) for instructions.
+:::
 
 Note that if the required arguments for `nf-core create` are not given, it will interactively prompt for them. If you prefer, you can supply them as command line arguments. See `nf-core create --help` for more information.
 
@@ -968,7 +978,9 @@ before_command: sed 's/1.13a/1.10/g' modules/multiqc/main.nf > modules/multiqc/m
 
 To run unit tests of a module that you have installed or the test created by the command [`nf-core modules create-test-yml`](#create-a-module-test-config-file), you can use `nf-core modules test` command. This command runs the tests specified in `modules/tests/software/<tool>/<subtool>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).
 
-> This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new module to add the new files to your git index.
+:::info
+This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new module to add the new files to your git index.
+:::
 
 You can specify the module name in the form TOOL/SUBTOOL in command line or provide it later by prompts.
 
@@ -1241,7 +1253,9 @@ extra_env:
 
 To run unit tests of a subworkflow that you have installed or the test created by the command [`nf-core subworkflow create-test-yml`](#create-a-subworkflow-test-config-file), you can use `nf-core subworkflows test` command. This command runs the tests specified in `tests/subworkflows/<subworkflow_name>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).
 
-> This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new subworkflow to add the new files to your git index.
+:::info
+This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new subworkflow to add the new files to your git index.
+:::
 
 You can specify the subworkflow name in the form TOOL/SUBTOOL in command line or provide it later by prompts.
 
diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md
index ecdda0f86..6a1b9a917 100644
--- a/nf_core/pipeline-template/.github/CONTRIBUTING.md
+++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md
@@ -11,7 +11,9 @@ Contributions to the code are even more welcome ;)
 
 {% if branded -%}
 
-> If you need help using or modifying {{ name }} then the best place to ask is on the nf-core Slack [#{{ short_name }}](https://nfcore.slack.com/channels/{{ short_name }}) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying {{ name }} then the best place to ask is on the nf-core Slack [#{{ short_name }}](https://nfcore.slack.com/channels/{{ short_name }}) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::
 
 {% endif -%}
 
diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md
index 6342823b1..6dba3032a 100644
--- a/nf_core/pipeline-template/docs/usage.md
+++ b/nf_core/pipeline-template/docs/usage.md
@@ -79,7 +79,9 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
-> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+:::warning
+Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+:::
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -116,7 +118,9 @@ This version number will be logged in reports when you run the pipeline, so that
 
 To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
-> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+:::tip
+If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+:::
 
 ## Core Nextflow arguments
 
@@ -130,7 +134,9 @@ Use this parameter to choose a configuration profile. Profiles can give configur
 
 Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
-> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+:::info
+We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+:::
 
 {%- if nf_core_configs %}