Merge pull request #2742 from mirpedrol/pipelines-create-docs

nf-core/tools v3.0.0 preparation: update docs for new command nf-core pipelines create

sites/docs/package.json

@@ -14,15 +14,16 @@
         "test": "playwright test"
     },
     "dependencies": {
-        "@astrojs/mdx": "^3.1.3",
-        "@astrojs/netlify": "^5.4.0",
-        "@iconify-json/fa": "^1.1.8",
-        "@iconify-json/fa-brands": "^1.1.8",
-        "@iconify-json/file-icons": "^1.1.9",
-        "@iconify-json/logos": "^1.1.43",
-        "@iconify-json/mdi": "^1.1.67",
-        "@iconify-json/octicon": "^1.1.56",
-        "@iconify/utils": "^2.1.25",
-        "svelte-exmarkdown": "^3.0.5"
+        "@astrojs/mdx": "^3.1.7",
+        "@astrojs/netlify": "^5.5.3",
+        "@iconify-json/fa": "^1.2.0",
+        "@iconify-json/fa-brands": "^1.2.0",
+        "@iconify-json/file-icons": "^1.2.0",
+        "@iconify-json/logos": "^1.2.0",
+        "@iconify-json/mdi": "^1.2.0",
+        "@iconify-json/octicon": "^1.2.0",
+        "@iconify/utils": "^2.1.33",
+        "svelte-exmarkdown": "^3.0.5",
+        "yaml": "^2.5.1"
     }
 }

sites/docs/src/content/docs/checklists/pipeline_release.md

@@ -12,7 +12,7 @@ If this is your first release, make sure to follow the [first release tutorial](
 
 1. [ ] Check the pipeline follows [nf-core guidelines](/docs/guidelines/pipelines/overview).
 2. [ ] All continuous-integration tests on the `dev` branch should be passing
-   - [ ] Check the output of `nf-core lint` for warnings and address all that you can
+   - [ ] Check the output of `nf-core pipelines lint` for warnings and address all that you can
    - [ ] Update any software dependencies that are out of date.
          The linting will warn about available updates via automated API calls to (bio-)conda
 3. [ ] Check that there are no outstanding issues that need to be addressed, especially bug reports.
@@ -25,11 +25,11 @@ If this is your first release, make sure to follow the [first release tutorial](
 
 1. [ ] On your fork, bump the version number of the `dev` branch to a release version
    - [ ] For example, `1.0.0dev` becomes `1.0.0`
-   - [ ] Use the `nf-core bump-version` command to make the changes, eg: navigate to the pipeline directory and run `nf-core bump-version 1.0.0`
+   - [ ] Use the `nf-core pipelines bump-version` command to make the changes, eg: navigate to the pipeline directory and run `nf-core pipelines bump-version 1.0.0`
    - [ ] Please make sure to use strictly numeric release numbers
    - [ ] Use [Semantic Versioning](https://semver.org/)
    - [ ] Make sure to update the version in any pipeline diagrams and other figures
-2. [ ] Run `nf-core lint --release` and check that there are no test failures for release.
+2. [ ] Run `nf-core pipelines lint --release` and check that there are no test failures for release.
 3. [ ] Check that `CHANGELOG.md` includes everything that has been added/fixed in this release, update the version number above the changes, and optionally add a human-readable release name (e.g. using a [code name generator](http://www.codenamegenerator.com/))
    - [ ] We recommend you also add the GitHub handle of the main contributors of each CHANGELOG entry (author, and significant reviewers etc.). This will mean each release on GitHub will display each contributors icons for extra visibility and recognition.
 4. [ ] [Open a Pull Request (PR)](https://help.github.com/en/articles/creating-a-pull-request) with these changes from your fork to the `dev` branch on the nf-core repository.
@@ -62,7 +62,7 @@ The last step is to bump up the pipeline version number in the development branc
 1. [ ] Make sure the dev branch on your fork is up to date
 2. [ ] On a new branch, bump to a new `dev` version
    - [ ] For example, `1.0.0` becomes `1.1.0dev`
-   - [ ] Use the `nf-core bump-version` command to make the changes, eg: navigate to the pipeline directory and run `nf-core bump-version 1.1.0dev`
+   - [ ] Use the `nf-core pipelines bump-version` command to make the changes, eg: navigate to the pipeline directory and run `nf-core pipelines bump-version 1.1.0dev`
 3. [ ] Update the `CHANGELOG.md` to include a new section for this new version
 4. [ ] [Open a Pull Request (PR)](https://help.github.com/en/articles/creating-a-pull-request) with these changes from your fork to the `dev` branch on the nf-core repository.
 5. [ ] (first release only) After the first release of the pipeline you will need to add the DOI manually into the main `README.md` for the pipeline:

sites/docs/src/content/docs/contributing/pipelines/pipeline_file_structure.md

@@ -12,14 +12,14 @@ describing what each file is and what it does.
 
 ## Files
 
-You will find the following files in each nf-core pipeline. They are automatically generated, when running `nf-core create`.
+You will find the following files in each nf-core pipeline. They are automatically generated, when running `nf-core pipelines create`.
 
 | Filename               | Description                                                                                                                                                                                                                                                                                                                                                                                         |
 | ---------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `main.nf`              | This is the main nextflow file which will get executed if the pipeline is run. Typically, parameters are initialized and validated in this script before a workflow from the `workflows/` directory is called for execution.                                                                                                                                                                        |
 | `nextflow.config`      | The main nextflow configuration file. It contains the default pipeline parameters, nextflow configuration options and information like pipeline and minimum nextflow version, among others. The `nextflow.config` also defines different configuration profiles that can be used to run the pipeline. See the [Configuration docs](/docs/usage/getting_started/configuration) for more information. |
 | `README.md`            | Basic information about the pipeline and usage                                                                                                                                                                                                                                                                                                                                                      |
-| `nextflow_schema.json` | The JSON schema file is used for pipeline parameter specification. This is automatically created using the `nf-core schema build` command. It is used for printing command-line help, validating input parameters, building the website docs and for building pipeline launch interfaces (web and cli).                                                                                             |
+| `nextflow_schema.json` | The JSON schema file is used for pipeline parameter specification. This is automatically created using the `nf-core pipelines schema build` command. It is used for printing command-line help, validating input parameters, building the website docs and for building pipeline launch interfaces (web and cli).                                                                                   |
 | `CHANGELOG.md`         | Information about the changes made to the pipeline for each release.                                                                                                                                                                                                                                                                                                                                |
 | `LICENSE`              | The license - should be MIT                                                                                                                                                                                                                                                                                                                                                                         |
 | `CODE_OF_CONDUCT.md`   | The nf-core code of conduct.                                                                                                                                                                                                                                                                                                                                                                        |

sites/docs/src/content/docs/guidelines/graphic_design.md

@@ -21,7 +21,7 @@ All information for the nf-core logo can be seen at the [nf-core/logos GitHub re
 | Monochrome - dark background | <img class="bg-dark d-block p-2" src="https://raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-mono-white.png" width="300"> | [PNG](https://github.com/nf-core/logos/blob/master/nf-core-logos/nf-core-logo-mono-white.png) <br> [SVG](https://github.com/nf-core/logos/blob/master/nf-core-logos/nf-core-logo-mono-white.svg) <br> [Adobe Illustrator `.ai`](https://github.com/nf-core/logos/blob/master/nf-core-logos/nf-core-logo-mono-white.ai) |
 | Square                       | <img src="https://raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-square.png" width="60">                                  | [PNG](https://github.com/nf-core/logos/blob/master/nf-core-logos/nf-core-logo-square.png) <br> [SVG](https://github.com/nf-core/logos/blob/master/nf-core-logos/nf-core-logo-square.svg) <br> [Adobe Illustrator `.ai`](https://github.com/nf-core/logos/blob/master/nf-core-logos/nf-core-logo-square.ai)             |
 
-The `nf-core create` command will generate a logo for your pipeline automatically.
+The `nf-core pipelines create` command will generate a logo for your pipeline automatically.
 However, you can also do this yourself by visiting [https://nf-co.re/logo/pipelinename](https://nf-co.re/logo/pipelinename), where `pipelinename` can be anything.
 
 Please note that nf-core is a separate entity from Nextflow.

sites/docs/src/content/docs/guidelines/pipelines/overview.md

@@ -50,7 +50,7 @@ All nf-core pipelines _must_ follow the following guidelines:
 - [Standardised parameters](/docs/guidelines/pipelines/requirements/parameters): Strive to have standardised usage.
 - [Single command](/docs/guidelines/pipelines/requirements/single_command): Pipelines should run in a single command.
 - [Keywords](/docs/guidelines/pipelines/requirements/keywords): Excellent documentation and GitHub repository keywords.
-- [Pass lint tests](/docs/guidelines/pipelines/requirements/linting): The pipeline must not have any failures in the `nf-core lint` tests.
+- [Pass lint tests](/docs/guidelines/pipelines/requirements/linting): The pipeline must not have any failures in the `nf-core pipelines lint` tests.
 - [Credits and Acknowledgements](/docs/guidelines/pipelines/requirements/acknowledgements): Pipelines must properly acknowledge prior work.
 - [Minimum inputs](/docs/guidelines/pipelines/requirements/minimum_inputs): Pipelines should be able to run with as little input as possible.
 - [Use nf-core git branches](/docs/guidelines/pipelines/requirements/git_branches): Use `master`, `dev` and `TEMPLATE`.
@@ -77,7 +77,7 @@ Indeed, numerous pipelines outside of nf-core now extensively use and contribute
 
 If using nf-core tools and especially the template, please don't call your pipeline `nf-core/<yourpipeline>`.
 Please say that your pipeline _"uses"_ nf-core rather than rather than _"is"_ nf-core.
-Remember that you can generate a pipeline with `nf-core create` that excludes nf-core branding.
+Remember that you can generate a pipeline with `nf-core pipelines create` that excludes nf-core branding.
 Citation and acknowledgement of the work that goes into these tools and templates is welcome.
 
 > Non nf-core pipelines can be added to [nextflow-io/awesome-nextflow](https://github.com/nextflow-io/awesome-nextflow) for added visibility.

sites/docs/src/content/docs/guidelines/pipelines/requirements/linting.md

@@ -1,14 +1,14 @@
 ---
 title: Pass lint tests
-subtitle: The pipeline must not have any failures in the `nf-core lint` tests
+subtitle: The pipeline must not have any failures in the `nf-core pipelines lint` tests
 menu:
   main:
     weight: 130
 ---
 
 In order to automate and standardise the nf-core best practices, we have built a code linting tool.
 These tests are run by the [nf-core/tools](https://github.com/nf-core/tools) package.
-The `nf-core lint` command must be run by continuous integration tests on GitHub Actions and must be passing before release.
+The `nf-core pipelines lint` command must be run by continuous integration tests on GitHub Actions and must be passing before release.
 
 You can see the list of tests and how to pass them on the [error codes page](https://nf-co.re/tools).
 

sites/docs/src/content/docs/guidelines/pipelines/requirements/use_the_template.md

@@ -8,7 +8,7 @@ menu:
 
 All nf-core pipelines must be built using the nf-core template.
 
-Workflows should be started using the `nf-core create` command which makes a new git repository and the initial commits and branches.
+Workflows should be started using the `nf-core pipelines create` command which makes a new git repository and the initial commits and branches.
 This is to ensure that the automated sync process that keeps all nf-core pipelines up to date can work. See the [sync docs](/docs/tutorials/sync/overview) for details.
 
 Where possible, workflow authors should do their best to follow nf-core conventions for filenames and code locations.

sites/docs/src/content/docs/nf-core-tools/pipelines/bump-version.md

@@ -5,16 +5,16 @@ shortTitle: bump-version
 weight: 90
 ---
 
-When releasing a new version of a nf-core pipeline, version numbers have to be updated in several different places. The helper command `nf-core bump-version` automates this for you to avoid manual errors (and frustration!).
+When releasing a new version of a nf-core pipeline, version numbers have to be updated in several different places. The helper command `nf-core pipelines bump-version` automates this for you to avoid manual errors (and frustration!).
 
 The command uses results from the linting process, so will only work with workflows that pass these tests.
 
-Usage is `nf-core bump-version <new_version>`, eg:
+Usage is `nf-core pipelines bump-version <new_version>`, eg:
 
 <!-- RICH-CODEX
 working_dir: tmp/nf-core-nextbigthing
 -->
 
-![`nf-core bump-version 1.1`](/images/tools/nf-core-bump-version.svg)
+![`nf-core pipelines bump-version 1.1`](/images/tools/nf-core-bump-version.svg)
 
 You can change the directory from the current working directory by specifying `--dir <pipeline_dir>`. To change the required version of Nextflow instead of the pipeline version number, use the flag `--nextflow`.

sites/docs/src/content/docs/nf-core-tools/pipelines/create-logo.md

@@ -5,12 +5,12 @@ shortTitle: create-logo
 weight: 110
 ---
 
-The `nf-core create-logo` command creates a logo for your pipeline based on the nf-core template and the pipeline name. You can specify the width of the logo in pixels with the `--width` flag. Additionally, you can specify the output format to be either `png` or `svg` with the `--format` flag. The default format is `png`.
+The `nf-core pipelines create-logo` command creates a logo for your pipeline based on the nf-core template and the pipeline name. You can specify the width of the logo in pixels with the `--width` flag. Additionally, you can specify the output format to be either `png` or `svg` with the `--format` flag. The default format is `png`.
 
-Usage is `nf-core create-logo <text>`, eg:
+Usage is `nf-core pipelines create-logo <text>`, eg:
 
 <!-- RICH-CODEX
 working_dir: tmp
 -->
 
-![`nf-core create-logo nextbigthing`](/images/tools/nf-core-create-logo.svg)
+![`nf-core pipelines create-logo nextbigthing`](/images/tools/nf-core-create-logo.svg)

sites/docs/src/content/docs/nf-core-tools/pipelines/create-params-file.md

@@ -6,9 +6,9 @@ weight: 30
 ---
 
 Sometimes it is easier to manually edit a parameter file than to use the web interface or interactive commandline wizard
-provided by `nf-core launch`, for example when running a pipeline with many options on a remote server without a graphical interface.
+provided by `nf-core pipelines launch`, for example when running a pipeline with many options on a remote server without a graphical interface.
 
-You can create a parameter file with all parameters of a pipeline with the `nf-core create-params-file` command.
+You can create a parameter file with all parameters of a pipeline with the `nf-core pipelines create-params-file` command.
 This file can then be passed to `nextflow` with the `-params-file` flag.
 
 This command takes one argument - either the name of a nf-core pipeline which will be pulled automatically,