From 29738a0885167b56d76660367b02bc506def39fe Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 8 Oct 2024 13:08:12 +0200 Subject: [PATCH] =?UTF-8?q?asciinema=20=F0=9F=91=8E=F0=9F=8F=BB=20yotube?= =?UTF-8?q?=20=F0=9F=91=8D=F0=9F=8F=BB?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../2024/{tools-3_0_0.md => tools-3_0_0.mdx} | 138 +++++++++--------- 1 file changed, 70 insertions(+), 68 deletions(-) rename sites/main-site/src/content/blog/2024/{tools-3_0_0.md => tools-3_0_0.mdx} (66%) diff --git a/sites/main-site/src/content/blog/2024/tools-3_0_0.md b/sites/main-site/src/content/blog/2024/tools-3_0_0.mdx similarity index 66% rename from sites/main-site/src/content/blog/2024/tools-3_0_0.md rename to sites/main-site/src/content/blog/2024/tools-3_0_0.mdx index a14ef445e4..661e5d0ece 100644 --- a/sites/main-site/src/content/blog/2024/tools-3_0_0.md +++ b/sites/main-site/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). - -- 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). + +- 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 ```