asciinema 👎🏻 yotube 👍🏻

nf-core · Oct 8, 2024 · 29738a0 · 29738a0
1 parent b988f58
commit 29738a0
Showing 1 changed file with 70 additions and 68 deletions.
diff --git a/...site/src/content/blog/2024/tools-3_0_0.md → ...ite/src/content/blog/2024/tools-3_0_0.mdx b/...site/src/content/blog/2024/tools-3_0_0.md → ...ite/src/content/blog/2024/tools-3_0_0.mdx
@@ -5,14 +5,16 @@ headerImage: 'https://images.unsplash.com/photo-1583258292688-d0213dc5a3a8'
 headerImageAlt: 'Shelves of yellow and red apples on display in a supermarket'
 pubDate: 2024-10-07T14:00:00+01:00
 authors:
-  - 'mirpedrol'
-  - 'mashehu'
-  - 'ewels'
+    - 'mirpedrol'
+    - 'mashehu'
+    - 'ewels'
 label:
-  - 'tools'
+    - 'tools'
 maxHeadingDepth: 3
 ---
 
+import { YouTube } from '@astro-community/astro-embed-youtube';
+
 # What and Why?
 
 The nf-core/tools CLI is the backbone of our community.
@@ -28,51 +30,51 @@ We promise, it's worth it! :pray:
 
 ## ✨ New features
 
-- Enhanced pipeline template customisation
-  - The template has been divided into features that can be selectively included or excluded.
-    For example, you can now create a new pipeline without any traces of FastQC.
-  - You can strip down the pipeline to the bare minimum and add only the tools you need.
-  - For nf-core pipelines, certain core features (e.g., documentation, CI tests) remain mandatory, but you still have significant customisation flexibility.
-- New Text User Interface (TUI) for pipeline creation
-  - A guided interface helps you through the process when running `nf-core pipelines create{:bash}` (don't worry - you can still use the CLI by providing all values as parameters).
-  <script src="https://asciinema.org/a/Qm4ulzsK9m6WaCcDPyh96khfh.js" id="asciicast-Qm4ulzsK9m6WaCcDPyh96khfh" async="true"></script>
-- Switch to [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) for input validation
-  - Replaces its predecessor nf-validation as a standard plugin in the template
-- CI tests now use the nf-core tools version matching the pipeline's template version
-  - This will reduce errors in opened PRs with each new tools release
+-   Enhanced pipeline template customisation
+    -   The template has been divided into features that can be selectively included or excluded.
+        For example, you can now create a new pipeline without any traces of FastQC.
+    -   You can strip down the pipeline to the bare minimum and add only the tools you need.
+    -   For nf-core pipelines, certain core features (e.g., documentation, CI tests) remain mandatory, but you still have significant customisation flexibility.
+-   New Text User Interface (TUI) for pipeline creation
+    -   A guided interface helps you through the process when running `nf-core pipelines create{:bash}` (don't worry - you can still use the CLI by providing all values as parameters).
+        <YouTube id={'VwjXNXONHlY'} poster={`https://img.youtube.com/vi/VwjXNXONHlY/maxresdefault.jpg`} />
+-   Switch to [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) for input validation
+    -   Replaces its predecessor nf-validation as a standard plugin in the template
+-   CI tests now use the nf-core tools version matching the pipeline's template version
+    -   This will reduce errors in opened PRs with each new tools release
 
 ## ⛓️‍💥 Breaking changes
 
-- All pipeline commands now require the `pipelines` prefix.
-  This change makes the commands more consistent with `nf-core modules{:bash}` and `nf-core subworkflows{:bash}` commands.
-  The commands which changed are:
-
-  | old command                         | new command                                   |
-  | ----------------------------------- | --------------------------------------------- |
-  | `nf-core lint{:bash}`               | `nf-core pipelines lint{:bash}`               |
-  | `nf-core launch{:bash}`             | `nf-core pipelines launch{:bash}`             |
-  | `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}`       |
-  | `nf-core schema docs{:bash}`        | `nf-core pipelines schema docs{:bash}`        |
-  | `nf-core schema lint{:bash}`        | `nf-core pipelines schema lint{:bash}`        |
-  | `nf-core schema validate{:bash}`    | `nf-core pipelines schema validate{:bash}`    |
-  | `nf-core create-logo{:bash}`        | `nf-core pipelines create-logo{:bash}`        |
-
-- Some options have been changed for the `nf-core pipelines download{:bash}` command:
-  - The `-t` / `--tower` flag has been renamed to `-p` / `--platform`.
-  - We renamed the short flags for consistency, to always use the first letter of the second word in the long flag:
-    - The `-d` / `--download-configuration` flag has been renamed to `-c` / `--download-configuration`.
-    - The `-p` / `--parallel-downloads` flag has been renamed to `-d` / `--parallel-downloads`.
+-   All pipeline commands now require the `pipelines` prefix.
+    This change makes the commands more consistent with `nf-core modules{:bash}` and `nf-core subworkflows{:bash}` commands.
+    The commands which changed are:
+
+    | old command                         | new command                                   |
+    | ----------------------------------- | --------------------------------------------- |
+    | `nf-core lint{:bash}`               | `nf-core pipelines lint{:bash}`               |
+    | `nf-core launch{:bash}`             | `nf-core pipelines launch{:bash}`             |
+    | `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}`       |
+    | `nf-core schema docs{:bash}`        | `nf-core pipelines schema docs{:bash}`        |
+    | `nf-core schema lint{:bash}`        | `nf-core pipelines schema lint{:bash}`        |
+    | `nf-core schema validate{:bash}`    | `nf-core pipelines schema validate{:bash}`    |
+    | `nf-core create-logo{:bash}`        | `nf-core pipelines create-logo{:bash}`        |
+
+-   Some options have been changed for the `nf-core pipelines download{:bash}` command:
+    -   The `-t` / `--tower` flag has been renamed to `-p` / `--platform`.
+    -   We renamed the short flags for consistency, to always use the first letter of the second word in the long flag:
+        -   The `-d` / `--download-configuration` flag has been renamed to `-c` / `--download-configuration`.
+        -   The `-p` / `--parallel-downloads` flag has been renamed to `-d` / `--parallel-downloads`.
 
 ## 🫡 Deprecations
 
-- The `nf-core licences{:bash}` command is deprecated.
-- Python 3.8 reaches end of life in October 2024, so this will probably be the last release supporting Python 3.8.
+-   The `nf-core licences{:bash}` command is deprecated.
+-   Python 3.8 reaches end of life in October 2024, so this will probably be the last release supporting Python 3.8.
 
 # Tip: Avoiding Merge Conflicts
 
@@ -82,10 +84,10 @@ Doing so means less code will update in the template, and fewer merge conflicts
 
 So - if you don't use any of these template features:
 
-- fastqc
-- multiqc
-- igenomes
-- nf_schema
+-   fastqc
+-   multiqc
+-   igenomes
+-   nf_schema
 
 you can minimize merge conflicts with a quick update and intermediate sync:
 
@@ -111,10 +113,10 @@ git checkout TEMPLATE -- .nf-core.yml
 
 ```yaml title=".nf-core.yml"
 template:
-  skip_features:
-    - fastqc
-    - igenomes
-    - nf_schema
+    skip_features:
+        - fastqc
+        - igenomes
+        - nf_schema
 ```
 
 5. Commit the changes:
@@ -144,11 +146,11 @@ This plugin uses a new JSON schema draft (2020-12), requiring changes to the `ne
 
 The following validation parameters have been removed from `nextflow.config` and `nextflow_schema.json`:
 
-- `validationFailUnrecognisedParams`
-- `validationLenientMode`
-- `validationSchemaIgnoreParams`
-- `validationShowHiddenParams`
-- `validate_params`
+-   `validationFailUnrecognisedParams`
+-   `validationLenientMode`
+-   `validationSchemaIgnoreParams`
+-   `validationShowHiddenParams`
+-   `validate_params`
 
 Instead, use the `validation` scope for `nf-schema` options.
 
@@ -162,9 +164,9 @@ The `UTILS_NFVALIDATION_PLUGIN` subworkflow has been replaced by `UTILS_NFSCHEMA
 
 To prepare for upcoming Nextflow syntax depreciations, for loops and try/catch blocks have been removed from the template config files:
 
-- nf-core configs are now included without try/catch blocks
-- Include statements have been moved after profile definitions to ensure correct profile overriding
-- For more information, see these Nextflow issues: [#1792](https://github.com/nextflow-io/nextflow/issues/1792) and [#5306](https://github.com/nextflow-io/nextflow/issues/5306)
+-   nf-core configs are now included without try/catch blocks
+-   Include statements have been moved after profile definitions to ensure correct profile overriding
+-   For more information, see these Nextflow issues: [#1792](https://github.com/nextflow-io/nextflow/issues/1792) and [#5306](https://github.com/nextflow-io/nextflow/issues/5306)
 
 # Common Merge Conflicts and Solutions
 
@@ -244,15 +246,15 @@ lint: null
 nf_core_version: 3.0.0
 org_path: null
 template:
-  author: Author Name
-  description: The description of the pipeline
-  force: false
-  is_nfcore: true
-  name: pipelinename
-  org: nf-core
-  outdir: .
-  skip_features: []
-  version: 3.0.0
+    author: Author Name
+    description: The description of the pipeline
+    force: false
+    is_nfcore: true
+    name: pipelinename
+    org: nf-core
+    outdir: .
+    skip_features: []
+    version: 3.0.0
 update: null
 ```