docs: adding missing pipelines cli prefix

sites/docs/src/content/api_reference/3.0.0/api/pipelines/create.md

@@ -33,7 +33,7 @@ See also \[the Screen.SUB_TITLE attribute]\[textual.screen.Screen.SUB_TITLE].
 
 #### `TEMPLATE_CONFIG{:python}`_= CreateConfig(org=None, name=None, description=None, author=None, version=None, force=True, outdir=None, skip_features=None, is_nfcore=None)_
 
-#### `TITLE{:python}`_: str | None_ _= 'nf-core create'_
+#### `TITLE{:python}`_: str | None_ _= 'nf-core pipelines create'_
 
 A class variable to set the _default_ title for the application.
 

sites/docs/src/content/api_reference/3.0.1/api/pipelines/create.md

@@ -33,7 +33,7 @@ See also \[the Screen.SUB_TITLE attribute]\[textual.screen.Screen.SUB_TITLE].
 
 #### `TEMPLATE_CONFIG{:python}`_= CreateConfig(org=None, name=None, description=None, author=None, version=None, force=True, outdir=None, skip_features=None, is_nfcore=None)_
 
-#### `TITLE{:python}`_: str | None_ _= 'nf-core create'_
+#### `TITLE{:python}`_: str | None_ _= 'nf-core pipelines create'_
 
 A class variable to set the _default_ title for the application.
 

sites/docs/src/content/api_reference/3.0.1/pipeline_lint_tests/template_strings.md

@@ -4,7 +4,7 @@
 
 Check for template placeholders.
 
-The `nf-core create` pipeline template uses
+The `nf-core pipelines create` pipeline template uses
 [Jinja](https://jinja.palletsprojects.com/en/2.11.x/) behind the scenes.
 
 This lint test fails if any Jinja template variables such as

sites/docs/src/content/docs/nf-core-tools/CLI/pipelines/create.mdx

@@ -13,7 +13,7 @@ With a given pipeline name, description and author, it makes a starter pipeline
 After creating the files, the command initialises the folder as a git repository and makes an initial commit.
 This first "vanilla" commit which is identical to the output from the templating tool is important, as it allows us to keep your pipeline in sync with the base template in the future.
 A full description of the file structure and all files created in the initial pipeline setup can be found [here](https://nf-co.re/docs/contributing/pipelines/pipeline_file_structure).
-See the [nf-core syncing docs](https://nf-co.re/docs/tutorials/sync/overview) for more information on how the syncing works.
+See the [nf-core pipelines sync docs](https://nf-co.re/docs/tutorials/sync/overview) for more information on how the syncing works.
 
 ![` nf-core pipelines create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" -a "Big Steve" --plain`](../../../../../assets/images/tools/nf-core-create.svg)
 

sites/docs/src/content/docs/nf-core-tools/CLI/pipelines/lint.md

@@ -15,7 +15,7 @@ timeout: 60
 working_dir: tmp/nf-core-nextbigthing
 before_command: >
   echo "lint: { pipeline_todos: false }" >> .nf-core.yml
-fake_command: nf-core lint
+fake_command: nf-core pipelines lint
 -->
 
 ![`nf-core pipelines lint`](../../../../../assets/images/tools/nf-core-lint.svg)

sites/docs/src/content/docs/nf-core-tools/CLI/pipelines/schema.md

@@ -9,7 +9,7 @@ nf-core pipelines have a `nextflow_schema.json` file in their root that describe
 These files enable automated input validation, generate command line help, and build interfaces to launch pipelines.
 Pipeline schema files follow the [JSONSchema specification](https://json-schema.org/) (Draft 7).
 
-To help developers working with pipeline schema, nf-core tools has three `schema` sub-commands:
+To help developers working with pipeline schema, nf-core tools has four `schema` sub-commands:
 
 - `nf-core pipelines schema validate`
 - `nf-core pipelines schema build`
@@ -36,14 +36,14 @@ The `pipeline` option can be a directory containing a pipeline, a path to a sche
 
 ## Build a pipeline schema
 
-Manually building JSONSchema documents is complex and error prone.
+Manually building JSONSchema documents is complex and error-prone.
 The `nf-core pipelines schema build` command collects your pipeline parameters and provides interactive prompts about any missing or unexpected parameters.
 If no schema exists, it will create one for you.
 
 Once built, the tool can send the schema to the nf-core website where you can use a graphical interface to organise and fill in the schema.
 The tool checks your schema status on the website and saves your changes locally once complete.
 
-Run `nf-core schema build -d <pipeline-directory>`, for example:
+Run `nf-core pipelines schema build -d <pipeline-directory>`, for example:
 
 <!-- RICH-CODEX
 working_dir: tmp/nf-core-nextbigthing

sites/docs/src/content/docs/specifications/configs/general.md

@@ -36,7 +36,7 @@ rather than pulling from public registries (e.g., Docker Hub, Quay.io).
 
 A config for infrastructure without external internet access SHOULD describe how to set
 `singularity.cacheDir` or `apptainer.cacheDir` to a directory pre-populated
-using [`nf-core download`](https://nf-co.re/docs/nf-core-tools/cli/pipelines/download) rather than configuring a container registry.
+using [`nf-core pipelines download`](https://nf-co.re/docs/nf-core-tools/cli/pipelines/download) rather than configuring a container registry.
 It SHOULD set `params.igenomes_ignore = true` and provide paths to locally
 available reference genomes instead.
 

sites/main-site/src/content/blog/2024/tools-3_0_0.mdx

@@ -57,7 +57,6 @@ We promise, it's worth it! :pray:
     | `nf-core download{:bash}`           | `nf-core pipelines download{:bash}`           |
     | `nf-core create-params-file{:bash}` | `nf-core pipelines create-params-file{:bash}` |
     | `nf-core create{:bash}`             | `nf-core pipelines create{:bash}`             |
-    | `nf-core lint{:bash}`               | `nf-core pipelines lint{:bash}`               |
     | `nf-core bump-version{:bash}`       | `nf-core pipelines bump-version{:bash}`       |
     | `nf-core sync{:bash}`               | `nf-core pipelines sync{:bash}`               |
     | `nf-core schema build{:bash}`       | `nf-core pipelines schema build{:bash}`       |

sites/main-site/src/content/blog/2025/tools-3_4_0.md

@@ -24,7 +24,7 @@ As always, if you have any problems or run into any bugs, reach out on the [#too
 
 ## Refactored download command
 
-The `nf-core download` command has received a major overhaul (see the [blog post](/blog/2025/refurbushing-the-pipeline-download) for more details about the motivation and new approach), bringing several powerful new features and improvements:
+The `nf-core pipelines download` command has received a major overhaul (see the [blog post](/blog/2025/refurbushing-the-pipeline-download) for more details about the motivation and new approach), bringing several powerful new features and improvements:
 
 #### Nextflow inspect for container discovery
 
@@ -43,7 +43,7 @@ With `nextflow inspect`, Nextflow itself tells us exactly which containers are u
 You can now download Docker images directly into tar archives, making it easier to transfer and deploy pipelines in air-gapped environments:
 
 ```bash /--compress tar/
-nf-core download <pipeline> --container-system docker --compress tar
+nf-core pipelines download <pipeline> --container-system docker --compress tar
 ```
 
 ## New devcontainer setup
@@ -73,7 +73,7 @@ If you want to bump the version of a series of modules which are based on the sa
 
 ```bash
 nf-core modules lint samtools
-nf-core bump-versions samtools
+nf-core modules bump-versions samtools
 ```
 
 Thank you [@nh13](https://github.com/nh13) for adding this feature!