Update some links

Author: christopher-hakkaart

sites/docs/src/content/docs/developing/components/cross-org-components.md

@@ -56,7 +56,3 @@ This enables the flexible syntax shown above.
   "minItems": 0
 },
 ```
-
-:::tip
-You can find a complete schema example in the [nf-core-test repository](https://github.com/nf-core/nf-core-test).
-:::

sites/docs/src/content/docs/developing/tutorials/writing-nf-core-modules/2-getting-started.md

@@ -19,7 +19,7 @@ You should already be familiar with:
 You need the following installed or set up:
 
 - [Nextflow](https://www.nextflow.io/docs/latest/install.html).
-- [nf-core tools](https://nf-co.re/docs/nf-core-tools/installation).
+- [nf-core tools](https://nf-co.re/docs/get_started/environment_setup/nf-core-tools).
 - A Nextflow-supported software management system, one of:
   - [Conda](https://conda-forge.org/download/)
   - [Docker](https://docs.docker.com/manuals/)

sites/docs/src/content/docs/developing/tutorials/writing-nf-core-modules/8-using.md

@@ -12,7 +12,7 @@ It assumes you have already contributed your module to the nf-core/modules repos
 
 ### Pipelines using the nf-core template
 
-If you generated your pipeline with [nf-core tools](https://nf-co.re/docs/nf-core-tools/pipelines/create) ([whether the pipeline is official or not](https://nf-co.re/docs/developing/pipelines/external-use)), you can install a module directly.
+If you generated your pipeline with [nf-core tools](https://nf-co.re/docs/nf-core-tools/pipelines/create) ([whether the pipeline is official or not](https://nf-co.re/docs/developing/external-use)), you can install a module directly.
 Run the following from the root of the repository, or pass `--dir`:
 
 ```bash

sites/docs/src/content/docs/running/configuration/configuration-options.md

@@ -54,7 +54,7 @@ nf-core provides these basic profiles for container engines:
 - `docker`: Uses [Docker](http://docker.com/) and pulls software from quay.io
 - `apptainer`: Uses [Singularity](https://apptainer.org/) and pulls software from quay.io
 - `podman`: Uses [Podman](https://podman.io/)
-- `shifter`: Uses [Shifter](https://www.nersc.gov/research-and-development/user-defined-images/)
+- `shifter`: Uses [Shifter](https://docs.nersc.gov/development/containers/shifter/how-to-use/)
 - `charliecloud`: Uses [Charliecloud](https://hpc.github.io/charliecloud/)
 - `conda`: Uses [Conda](https://conda.io/docs/) and pulls most software from [Bioconda](https://bioconda.github.io/)
 

sites/docs/src/content/docs/running/configuration/nextflow-for-your-system.md

@@ -193,7 +193,7 @@ For example, if you set `docker.registry = 'myregistry.com'`, the image pulls fr
 
 ## Update tool versions
 
-The [Nextflow DSL2](https://docs.seqera.io/nextflow/dsl2) implementation of nf-core pipelines uses one container or Conda environment per process, which simplifies software dependency maintenance and updates.
+The Nextflow DSL2 implementation of nf-core pipelines uses one container or Conda environment per process, which simplifies software dependency maintenance and updates.
 
 To use a different version of a tool, identify the `process` name and override the Nextflow `container` or `conda` definition for that process using the `withName` declaration.
 

sites/docs/src/content/docs/running/run-pipelines-offline.md

@@ -20,7 +20,7 @@ Running pipelines offline requires three main components:
 
 To transfer Nextflow to an offline system:
 
-1. [Install Nextflow](https://nextflow.io/docs/latest/getstarted.html#installation) in an online environment.
+1. [Install Nextflow](https://docs.seqera.io/nextflow/install) in an online environment.
 2. Run your pipeline locally.
 
    :::note

sites/docs/src/content/docs/running/run-pipelines.md

@@ -219,7 +219,7 @@ Always use `-resume` when re-running a pipeline after fixing errors or updating
 
 ### Notifications
 
-- Specify `--email your@email.com` to receive emails when your pipeline completes (requires Nextflow [mail and notification configuration](https://docs.seqera.io/nextflow/mail#mail-configuration)).
+- Specify `--email your@email.com` to receive emails when your pipeline completes (requires Nextflow [mail and notification configuration](https://docs.seqera.io/nextflow/notifications#mail)).
 - To receive notifications from your pipeline (e.g., on completion or failure), see the [nf-slack plugin](https://github.com/seqeralabs/nf-slack) for Slack or the [nf-teams plugin](https://github.com/nvnieuwk/nf-teams) for Microsoft Teams.
 
 ## Next steps

sites/docs/src/content/docs/specifications/components/modules/general.md

@@ -511,7 +511,7 @@ Alternative suggestions:
 ## Script inclusion
 
 Module templates separate scientific logic from workflow-specific logic, improving code clarity and maintainability.
-If a module's `script:` block contains a script rather than command invocations, regardless of the language (for example, Bash, R, Python), and the content is more than a readable length (as a rule of thumb, approximately 20 lines), provide it through a [Nextflow module template](https://docs.seqera.io/nextflow/module#module-templates).
+If a module's `script:` block contains a script rather than command invocations, regardless of the language (for example, Bash, R, Python), and the content is more than a readable length (as a rule of thumb, approximately 20 lines), provide it through a [Nextflow module template](https://docs.seqera.io/nextflow/process#template).
 
 :::note
 We recommend use of Nextflow templates as they are the most portable method of separating custom script content and execution across all execution contexts.

sites/main-site/src/content/events/2023/hackathon-march-2023/index.md

@@ -220,8 +220,8 @@ We will be a lot of people working in parallel during this hackathon, so to stay
    - Link it to the issue so that the issue closes when merged.
 6. :page_facing_up: Describe your work on the HackMD document for the project and tell the group! :tada:
 7. :memo: While waiting to receive a review - try reviewing someone else's PR!
-   - [Module review checklist](https://nf-co.re/docs/contributing/modules#new-module-guidelines-and-pr-review-checklist)
-   - [Subworkflow review checklist](https://nf-co.re/docs/contributing/subworkflows#new-subworkflow-guidelines-and-pr-review-checklist)
+   - [Module review checklist](https://nf-co.re/docs/contributing/reviewing-pull-requests/review_checklists/component)
+   - [Subworkflow review checklist](https://nf-co.re/docs/contributing/reviewing-pull-requests/review_checklists/component)
 8. :recycle: Repeat!
 
 > The HackMD document is the easiest to forget, but please add something even if you think what you did was small -