From 82373efcf9cfcf5ad0dd5e029e850d8ff69cb643 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 22 Apr 2024 15:30:46 +0200 Subject: [PATCH 1/5] add admonition about deprecation --- README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/README.md b/README.md index f2d611eb..78f764d0 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,16 @@ ## 📚 Docs 👉🏻 +> [!IMPORTANT] +> **`nf-validation` has now been renamed to `nf-schema`. The `nf-validation` plugin will not receive any future updates.** +> **Please update your pipelines to use [`nf-schema`](https://github.com/nextflow-io/nf-schema) instead.** +> +> This change was necessary to prevent older versions of `nf-core` pipelines from with unpinned plugin references from breaking when updating to the latest version of `nf-validation`. +> **Please pin the version of `nf-schema` in your pipeline's `nextflow.config` file:** +> ```nextflow +> plugins { id 'nf-schema@2.0.0' } +> ``` + **A Nextflow plugin to work with validation of pipeline parameters and sample sheets.** ## Introduction From a1f4ccaecb7370fef53eaee62fd869288fdf24c9 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 22 Apr 2024 15:31:08 +0200 Subject: [PATCH 2/5] add announcement about deprecation --- mkdocs.yml | 1 + overrides/main.html | 5 +++++ 2 files changed, 6 insertions(+) create mode 100644 overrides/main.html diff --git a/mkdocs.yml b/mkdocs.yml index f7242938..cb88d642 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -28,6 +28,7 @@ nav: theme: name: material + custom_dir: overrides icon: logo: octicons/checklist-16 repo: fontawesome/brands/github diff --git a/overrides/main.html b/overrides/main.html new file mode 100644 index 00000000..ed9985d6 --- /dev/null +++ b/overrides/main.html @@ -0,0 +1,5 @@ +{% extends "base.html" %} + +{% block announce %} +
nf-validation has been deprecated. Please use nf-schema instead.
+{% endblock %} \ No newline at end of file From 9ea2f3f8d18beef04e9a4abab6ad21a38168a86c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 22 Apr 2024 15:36:36 +0200 Subject: [PATCH 3/5] fix prettier --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 78f764d0..db4d6a88 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,7 @@ ## 📚 Docs 👉🏻 + > [!IMPORTANT] > **`nf-validation` has now been renamed to `nf-schema`. The `nf-validation` plugin will not receive any future updates.** > **Please update your pipelines to use [`nf-schema`](https://github.com/nextflow-io/nf-schema) instead.** From a07023184e36c3e72daa0a9066f43bfaa053c6fa Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 22 Apr 2024 17:12:17 +0200 Subject: [PATCH 4/5] Improve warnings style in mkdocs --- README.md | 6 ++++++ overrides/main.html | 7 +++++-- 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index db4d6a88..8f4b757c 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,10 @@ ## 📚 Docs 👉🏻 +!!! warning + +
+ > [!IMPORTANT] > **`nf-validation` has now been renamed to `nf-schema`. The `nf-validation` plugin will not receive any future updates.** @@ -13,6 +17,8 @@ > plugins { id 'nf-schema@2.0.0' } > ``` +
+ **A Nextflow plugin to work with validation of pipeline parameters and sample sheets.** ## Introduction diff --git a/overrides/main.html b/overrides/main.html index ed9985d6..87f89952 100644 --- a/overrides/main.html +++ b/overrides/main.html @@ -1,5 +1,8 @@ {% extends "base.html" %} {% block announce %} -
nf-validation has been deprecated. Please use nf-schema instead.
-{% endblock %} \ No newline at end of file +
+ nf-validation has been deprecated. + Please use nf-schema instead. +
+{% endblock %} From 53fd1bfdb4f0fe0bc8c733b669bf2789cced5752 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 22 Apr 2024 17:24:31 +0200 Subject: [PATCH 5/5] Get it working hopefully on both GitHub + mkdocs --- README.md | 8 +------- docs/index.md | 12 +++++++++++- 2 files changed, 12 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 8f4b757c..0009ff82 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,5 @@ # ![nf-validation](docs/images/nf-validation.svg) -## 📚 Docs 👉🏻 - -!!! warning - -
- > [!IMPORTANT] > **`nf-validation` has now been renamed to `nf-schema`. The `nf-validation` plugin will not receive any future updates.** @@ -17,7 +11,7 @@ > plugins { id 'nf-schema@2.0.0' } > ``` -
+## 📚 Docs 👉🏻 **A Nextflow plugin to work with validation of pipeline parameters and sample sheets.** diff --git a/docs/index.md b/docs/index.md index e9156893..f2a0f178 100644 --- a/docs/index.md +++ b/docs/index.md @@ -11,4 +11,14 @@ description: Nextflow plugin for sample sheet validation ==} ---8<-- "README.md:6:" +!!! warning "`nf-validation` has now been renamed to `nf-schema`." + + **`nf-validation` has now been renamed to `nf-schema`. The `nf-validation` plugin will not receive any future updates.** + **Please update your pipelines to use [`nf-schema`](https://github.com/nextflow-io/nf-schema) instead.** + This change was necessary to prevent older versions of `nf-core` pipelines from with unpinned plugin references from breaking when updating to the latest version of `nf-validation`. + **Please pin the version of `nf-schema` in your pipeline's `nextflow.config` file:** + ```nextflow + plugins { id 'nf-schema@2.0.0' } + ``` + +--8<-- "README.md:18:"