From 613cd3850c4e3fba9a949af60825f3143970119b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 26 Sep 2024 15:39:04 +0200 Subject: [PATCH 01/35] update docs fro new command nf-core pipelines create --- .../pipelines/{create.md => create.mdx} | 54 ++++++++++++++----- .../pages/docs/nf-core-tools/features.astro | 23 ++++++++ 2 files changed, 65 insertions(+), 12 deletions(-) rename sites/docs/src/content/docs/nf-core-tools/pipelines/{create.md => create.mdx} (54%) create mode 100644 sites/docs/src/pages/docs/nf-core-tools/features.astro diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/create.md b/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx similarity index 54% rename from sites/docs/src/content/docs/nf-core-tools/pipelines/create.md rename to sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx index 4a82c9d36a..46d61fc9dc 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/create.md +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx @@ -3,6 +3,7 @@ title: Creating a new pipeline subtitle: Scaffolding a new pipeline using the nf-core template shortTitle: create weight: 60 +import features from '../../../../pages/docs/nf-core-tools/features.astro' --- The `create` subcommand makes a new pipeline using the nf-core base template. @@ -23,17 +24,16 @@ You can then continue to edit, commit and push normally as you build your pipeli Please see the [nf-core documentation](/docs/tutorials/adding_a_pipeline/overview) for a full walkthrough of how to create a new nf-core workflow. > [!TIP] -> As the log output says, remember to come and discuss your idea for a pipeline as early as possible! +> As the command documentation says, remember to come and discuss your idea for a pipeline as early as possible! > See the [documentation](/docs/tutorials/adding_a_pipeline/move_to_nf-core_org) for instructions. -Note that if the required arguments for `nf-core create` are not given, it will interactively prompt for them. If you prefer, you can supply them as command line arguments. See `nf-core create --help` for more information. +If you prefer, you can supply them as command line arguments. See `nf-core pipelines create --help` for more information. ## Customization -The `nf-core create` command comes with a number of options that allow you to customize the creation of a pipeline if you intend to not publish it as an -nf-core pipeline. This can be done in two ways: by using interactive prompts, or by supplying a `template.yml` file using the `--template-yaml ` option. +The `nf-core pipelines create` command comes with a number of options that allow you to customize the creation of a pipeline. This can be done in two ways: by using the graphical interface, or by supplying a `template.yml` file using the `--template-yaml ` option. Both options allow you to specify a custom pipeline prefix to use instead of the common `nf-core`, as well as selecting parts of the template to be excluded during pipeline creation. -The interactive prompts will guide you through the pipeline creation process. An example of a `template.yml` file is shown below. +The interface will guide you through the pipeline creation process. Both nf-core and non-nf-core pipelines can be customised, but non-nf-core pipelines have more options which can be skipped. An example of a `template.yml` file is shown below. ```yaml name: coolpipe @@ -46,14 +46,44 @@ skip: - github_badges - igenomes - nf_core_configs +template: + author: me + description: A cool pipeline + force: false + is_nfcore: false + name: coolpipe + org: myorg + outdir: . + skip_features: + - github + - ci + - igenomes + - nf_core_configs + - code_linters + - citations + - gitpod + - codespaces + - multiqc + - fastqc + - modules + - changelog + - nf_schema + - license + - email + - adaptivecard + - slackreport + - documentation + - test_config + - seqera_platform + version: 1.0.0dev ``` -This will create a pipeline called `coolpipe` in the directory `myorg-coolpipe` (`-`) with `me` as the author. It will exclude all possible parts of the template: +This will create a pipeline called `coolpipe` in the directory `myorg-coolpipe` (`-`) with `me` as the author. It will exclude all possible parts of the template. + +A full list of possible features to skip from the template is described here: + + -- `github`: removed all files required for GitHub hosting of the pipeline. Specifically, the `.github` folder and `.gitignore` file. -- `ci`: removes the GitHub continuous integration tests from the pipeline. Specifically, the `.github/workflows/` folder. -- `github_badges`: removes GitHub badges from the `README.md` file. -- `igenomes`: removes pipeline options related to iGenomes. Including the `conf/igenomes.config` file and all references to it. -- `nf_core_configs`: excludes `nf_core/configs` repository options, which make multiple config profiles for various institutional clusters available. +To run the pipeline creation silently (i.e. without the graphical interface), you can provide all the arguments. The required ones are `--name`, `--description` and `--author`. -To run the pipeline creation silently (i.e. without any prompts) with the nf-core template, you can use the `--plain` option. +If you have an existing pipeline and you wish to add/exclude one fo the features. Don't use a `template.yml` file but modify the `.nf-core.yml` file from your pipeline and run `nf-core pipelines sync` to update the template. diff --git a/sites/docs/src/pages/docs/nf-core-tools/features.astro b/sites/docs/src/pages/docs/nf-core-tools/features.astro new file mode 100644 index 0000000000..f07355073e --- /dev/null +++ b/sites/docs/src/pages/docs/nf-core-tools/features.astro @@ -0,0 +1,23 @@ +--- +import yaml from 'js-yaml'; + +const yamlURL = 'https://raw.githubusercontent.com/nf-core/tools/refs/heads/dev/nf_core/pipelines/create/template_features.yml'; +const response = await fetch(yamlURL); +const yamlText = await response.text(); +const data = yaml.load(yamlText); + +const filteredData = Object.entries(data).map(([key, value]) => { + return { + key, + helpText: value.help_text || 'No help text available' + }; +}); +--- + +
    + {filteredData.map(({ key, helpText }) => ( +
  • + {key}: {helpText} +
    • + ))} +
From 6aaba59cb006ac542c05eb0be025237e57513617 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 26 Sep 2024 13:43:13 +0000 Subject: [PATCH 02/35] [automated] Fix code linting --- .../docs/nf-core-tools/pipelines/create.mdx | 68 +++++++++---------- .../pages/docs/nf-core-tools/features.astro | 23 ++++--- 2 files changed, 47 insertions(+), 44 deletions(-) diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx b/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx index 46d61fc9dc..650bb8e642 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx @@ -41,41 +41,41 @@ description: A cool pipeline author: me prefix: myorg skip: - - github - - ci - - github_badges - - igenomes - - nf_core_configs + - github + - ci + - github_badges + - igenomes + - nf_core_configs template: - author: me - description: A cool pipeline - force: false - is_nfcore: false - name: coolpipe - org: myorg - outdir: . - skip_features: - - github - - ci - - igenomes - - nf_core_configs - - code_linters - - citations - - gitpod - - codespaces - - multiqc - - fastqc - - modules - - changelog - - nf_schema - - license - - email - - adaptivecard - - slackreport - - documentation - - test_config - - seqera_platform - version: 1.0.0dev + author: me + description: A cool pipeline + force: false + is_nfcore: false + name: coolpipe + org: myorg + outdir: . + skip_features: + - github + - ci + - igenomes + - nf_core_configs + - code_linters + - citations + - gitpod + - codespaces + - multiqc + - fastqc + - modules + - changelog + - nf_schema + - license + - email + - adaptivecard + - slackreport + - documentation + - test_config + - seqera_platform + version: 1.0.0dev ``` This will create a pipeline called `coolpipe` in the directory `myorg-coolpipe` (`-`) with `me` as the author. It will exclude all possible parts of the template. diff --git a/sites/docs/src/pages/docs/nf-core-tools/features.astro b/sites/docs/src/pages/docs/nf-core-tools/features.astro index f07355073e..a0c5f58f87 100644 --- a/sites/docs/src/pages/docs/nf-core-tools/features.astro +++ b/sites/docs/src/pages/docs/nf-core-tools/features.astro @@ -1,23 +1,26 @@ --- import yaml from 'js-yaml'; -const yamlURL = 'https://raw.githubusercontent.com/nf-core/tools/refs/heads/dev/nf_core/pipelines/create/template_features.yml'; +const yamlURL = + 'https://raw.githubusercontent.com/nf-core/tools/refs/heads/dev/nf_core/pipelines/create/template_features.yml'; const response = await fetch(yamlURL); const yamlText = await response.text(); const data = yaml.load(yamlText); const filteredData = Object.entries(data).map(([key, value]) => { - return { - key, - helpText: value.help_text || 'No help text available' - }; + return { + key, + helpText: value.help_text || 'No help text available', + }; }); ---
    - {filteredData.map(({ key, helpText }) => ( -
  • - {key}: {helpText} -
    • - ))} + { + filteredData.map(({ key, helpText }) => ( +
  • + {key}: {helpText} +
    • + )) + }
From cb3446a9e1506652421ccde7fcd13ef71738bf8c Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 26 Sep 2024 16:09:57 +0200 Subject: [PATCH 03/35] update all nf-core commands to nf-core pipelnes --- .../docs/checklists/pipeline_release.md | 8 +++--- .../pipelines/pipeline_file_structure.md | 4 +-- .../content/docs/guidelines/graphic_design.md | 2 +- .../docs/guidelines/pipelines/overview.md | 4 +-- .../pipelines/requirements/linting.md | 4 +-- .../requirements/use_the_template.md | 2 +- .../nf-core-tools/pipelines/bump-version.md | 6 ++-- .../nf-core-tools/pipelines/create-logo.md | 6 ++-- .../pipelines/create-params-file.md | 4 +-- .../docs/nf-core-tools/pipelines/download.md | 12 ++++---- .../docs/nf-core-tools/pipelines/launch.md | 4 +-- .../docs/nf-core-tools/pipelines/licences.md | 2 +- .../docs/nf-core-tools/pipelines/lint.md | 8 +++--- .../docs/nf-core-tools/pipelines/list.md | 8 +++--- .../docs/nf-core-tools/pipelines/schema.md | 28 +++++++++---------- .../docs/nf-core-tools/pipelines/sync.md | 6 ++-- .../adding_a_pipeline/creating_a_pipeline.md | 6 ++-- .../adding_a_pipeline/first_release.md | 8 +++--- .../contributing_to_pipelines.md | 10 +++---- .../creating_with_nf-core.md | 12 ++++---- .../nf-core_contributing_overview.md | 24 ++++++++-------- .../sync/fixing_broken_template_branch.md | 4 +-- .../docs/tutorials/sync/manual_sync.md | 8 +++--- .../content/docs/tutorials/sync/overview.md | 10 +++---- .../tutorials/sync/sync_retrospectively.md | 4 +-- .../usage/Getting_started/introduction.md | 2 +- .../docs/usage/Getting_started/offline.md | 6 ++-- 27 files changed, 101 insertions(+), 101 deletions(-) diff --git a/sites/docs/src/content/docs/checklists/pipeline_release.md b/sites/docs/src/content/docs/checklists/pipeline_release.md index e0eb7f1b2e..4f3ba3a4bc 100644 --- a/sites/docs/src/content/docs/checklists/pipeline_release.md +++ b/sites/docs/src/content/docs/checklists/pipeline_release.md @@ -12,7 +12,7 @@ If this is your first release, make sure to follow the [first release tutorial]( 1. [ ] Check the pipeline follows [nf-core guidelines](/docs/guidelines/pipelines/overview). 2. [ ] All continuous-integration tests on the `dev` branch should be passing - - [ ] Check the output of `nf-core lint` for warnings and address all that you can + - [ ] Check the output of `nf-core pipelines lint` for warnings and address all that you can - [ ] Update any software dependencies that are out of date. The linting will warn about available updates via automated API calls to (bio-)conda 3. [ ] Check that there are no outstanding issues that need to be addressed, especially bug reports. @@ -25,10 +25,10 @@ If this is your first release, make sure to follow the [first release tutorial]( 1. [ ] On your fork, bump the version number of the `dev` branch to a release version - [ ] For example, `1.0.0dev` becomes `1.0.0` - - [ ] Use the `nf-core bump-version` command to make the changes, eg: navigate to the pipeline directory and run `nf-core bump-version 1.0.0` + - [ ] Use the `nf-core pipelines bump-version` command to make the changes, eg: navigate to the pipeline directory and run `nf-core pipelines bump-version 1.0.0` - [ ] Please make sure to use strictly numeric release numbers - [ ] Use [Semantic Versioning](https://semver.org/) -2. [ ] Run `nf-core lint --release` and check that there are no test failures for release. +2. [ ] Run `nf-core pipelines lint --release` and check that there are no test failures for release. 3. [ ] Check that `CHANGELOG.md` includes everything that has been added/fixed in this release, update the version number above the changes, and optionally add a human-readable release name (e.g. using a [code name generator](http://www.codenamegenerator.com/)) - [ ] We recommend you also add the GitHub handle of the main contributors of each CHANGELOG entry (author, and significant reviewers etc.). This will mean each release on GitHub will display each contributors icons for extra visibility and recognition. 4. [ ] [Open a Pull Request (PR)](https://help.github.com/en/articles/creating-a-pull-request) with these changes from your fork to the `dev` branch on the nf-core repository. @@ -61,7 +61,7 @@ The last step is to bump up the pipeline version number in the development branc 1. [ ] Make sure the dev branch on your fork is up to date 2. [ ] On a new branch, bump to a new `dev` version - [ ] For example, `1.0.0` becomes `1.1.0dev` - - [ ] Use the `nf-core bump-version` command to make the changes, eg: navigate to the pipeline directory and run `nf-core bump-version 1.1.0dev` + - [ ] Use the `nf-core pipelines bump-version` command to make the changes, eg: navigate to the pipeline directory and run `nf-core pipelines bump-version 1.1.0dev` 3. [ ] Update the `CHANGELOG.md` to include a new section for this new version 4. [ ] [Open a Pull Request (PR)](https://help.github.com/en/articles/creating-a-pull-request) with these changes from your fork to the `dev` branch on the nf-core repository. 5. [ ] (first release only) After the first release of the pipeline you will need to add the DOI manually into the main `README.md` for the pipeline: diff --git a/sites/docs/src/content/docs/contributing/pipelines/pipeline_file_structure.md b/sites/docs/src/content/docs/contributing/pipelines/pipeline_file_structure.md index 600b64585d..33653ffad1 100644 --- a/sites/docs/src/content/docs/contributing/pipelines/pipeline_file_structure.md +++ b/sites/docs/src/content/docs/contributing/pipelines/pipeline_file_structure.md @@ -12,14 +12,14 @@ describing what each file is and what it does. ## Files -You will find the following files in each nf-core pipeline. They are automatically generated, when running `nf-core create`. +You will find the following files in each nf-core pipeline. They are automatically generated, when running `nf-core pipelines create`. | Filename | Description  | | ---------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `main.nf` | This is the main nextflow file which will get executed if the pipeline is run. Typically, parameters are initialized and validated in this script before a workflow from the `workflows/` directory is called for execution. | | `nextflow.config` | The main nextflow configuration file. It contains the default pipeline parameters, nextflow configuration options and information like pipeline and minimum nextflow version, among others. The `nextflow.config` also defines different configuration profiles that can be used to run the pipeline. See the [Configuration docs](/docs/usage/getting_started/configuration) for more information. | | `README.md` | Basic information about the pipeline and usage | -| `nextflow_schema.json` | The JSON schema file is used for pipeline parameter specification. This is automatically created using the `nf-core schema build` command. It is used for printing command-line help, validating input parameters, building the website docs and for building pipeline launch interfaces (web and cli). | +| `nextflow_schema.json` | The JSON schema file is used for pipeline parameter specification. This is automatically created using the `nf-core pipelines schema build` command. It is used for printing command-line help, validating input parameters, building the website docs and for building pipeline launch interfaces (web and cli). | | `CHANGELOG.md` | Information about the changes made to the pipeline for each release. | | `LICENSE` | The license - should be MIT | | `CODE_OF_CONDUCT.md` | The nf-core code of conduct. | diff --git a/sites/docs/src/content/docs/guidelines/graphic_design.md b/sites/docs/src/content/docs/guidelines/graphic_design.md index 48c5230f65..8de2419891 100644 --- a/sites/docs/src/content/docs/guidelines/graphic_design.md +++ b/sites/docs/src/content/docs/guidelines/graphic_design.md @@ -21,7 +21,7 @@ All information for the nf-core logo can be seen at the [nf-core/logos GitHub re | Monochrome - dark background | | [PNG](https://github.com/nf-core/logos/blob/master/nf-core-logos/nf-core-logo-mono-white.png)
[SVG](https://github.com/nf-core/logos/blob/master/nf-core-logos/nf-core-logo-mono-white.svg)
[Adobe Illustrator `.ai`](https://github.com/nf-core/logos/blob/master/nf-core-logos/nf-core-logo-mono-white.ai) | | Square | | [PNG](https://github.com/nf-core/logos/blob/master/nf-core-logos/nf-core-logo-square.png)
[SVG](https://github.com/nf-core/logos/blob/master/nf-core-logos/nf-core-logo-square.svg)
[Adobe Illustrator `.ai`](https://github.com/nf-core/logos/blob/master/nf-core-logos/nf-core-logo-square.ai) | -The `nf-core create` command will generate a logo for your pipeline automatically. +The `nf-core pipelines create` command will generate a logo for your pipeline automatically. However, you can also do this yourself by visiting [https://nf-co.re/logo/pipelinename](https://nf-co.re/logo/pipelinename), where `pipelinename` can be anything. Please note that nf-core is a separate entity from Nextflow. diff --git a/sites/docs/src/content/docs/guidelines/pipelines/overview.md b/sites/docs/src/content/docs/guidelines/pipelines/overview.md index 2cb102b39f..af26a3266a 100644 --- a/sites/docs/src/content/docs/guidelines/pipelines/overview.md +++ b/sites/docs/src/content/docs/guidelines/pipelines/overview.md @@ -50,7 +50,7 @@ All nf-core pipelines _must_ follow the following guidelines: - [Standardised parameters](/docs/guidelines/pipelines/requirements/parameters): Strive to have standardised usage. - [Single command](/docs/guidelines/pipelines/requirements/single_command): Pipelines should run in a single command. - [Keywords](/docs/guidelines/pipelines/requirements/keywords): Excellent documentation and GitHub repository keywords. -- [Pass lint tests](/docs/guidelines/pipelines/requirements/linting): The pipeline must not have any failures in the `nf-core lint` tests. +- [Pass lint tests](/docs/guidelines/pipelines/requirements/linting): The pipeline must not have any failures in the `nf-core pipelines lint` tests. - [Credits and Acknowledgements](/docs/guidelines/pipelines/requirements/acknowledgements): Pipelines must properly acknowledge prior work. - [Minimum inputs](/docs/guidelines/pipelines/requirements/minimum_inputs): Pipelines should be able to run with as little input as possible. - [Use nf-core git branches](/docs/guidelines/pipelines/requirements/git_branches): Use `master`, `dev` and `TEMPLATE`. @@ -77,7 +77,7 @@ Indeed, numerous pipelines outside of nf-core now extensively use and contribute If using nf-core tools and especially the template, please don't call your pipeline `nf-core/`. Please say that your pipeline _"uses"_ nf-core rather than rather than _"is"_ nf-core. -Remember that you can generate a pipeline with `nf-core create` that excludes nf-core branding. +Remember that you can generate a pipeline with `nf-core pipelines create` that excludes nf-core branding. Citation and acknowledgement of the work that goes into these tools and templates is welcome. > Non nf-core pipelines can be added to [nextflow-io/awesome-nextflow](https://github.com/nextflow-io/awesome-nextflow) for added visibility. diff --git a/sites/docs/src/content/docs/guidelines/pipelines/requirements/linting.md b/sites/docs/src/content/docs/guidelines/pipelines/requirements/linting.md index 16bb668f35..6b0a149edb 100644 --- a/sites/docs/src/content/docs/guidelines/pipelines/requirements/linting.md +++ b/sites/docs/src/content/docs/guidelines/pipelines/requirements/linting.md @@ -1,6 +1,6 @@ --- title: Pass lint tests -subtitle: The pipeline must not have any failures in the `nf-core lint` tests +subtitle: The pipeline must not have any failures in the `nf-core pipelines lint` tests menu: main: weight: 130 @@ -8,7 +8,7 @@ menu: In order to automate and standardise the nf-core best practices, we have built a code linting tool. These tests are run by the [nf-core/tools](https://github.com/nf-core/tools) package. -The `nf-core lint` command must be run by continuous integration tests on GitHub Actions and must be passing before release. +The `nf-core pipelines lint` command must be run by continuous integration tests on GitHub Actions and must be passing before release. You can see the list of tests and how to pass them on the [error codes page](https://nf-co.re/tools). diff --git a/sites/docs/src/content/docs/guidelines/pipelines/requirements/use_the_template.md b/sites/docs/src/content/docs/guidelines/pipelines/requirements/use_the_template.md index 612f16e099..2304c70f9f 100644 --- a/sites/docs/src/content/docs/guidelines/pipelines/requirements/use_the_template.md +++ b/sites/docs/src/content/docs/guidelines/pipelines/requirements/use_the_template.md @@ -8,7 +8,7 @@ menu: All nf-core pipelines must be built using the nf-core template. -Workflows should be started using the `nf-core create` command which makes a new git repository and the initial commits and branches. +Workflows should be started using the `nf-core pipelines create` command which makes a new git repository and the initial commits and branches. This is to ensure that the automated sync process that keeps all nf-core pipelines up to date can work. See the [sync docs](/docs/tutorials/sync/overview) for details. Where possible, workflow authors should do their best to follow nf-core conventions for filenames and code locations. diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/bump-version.md b/sites/docs/src/content/docs/nf-core-tools/pipelines/bump-version.md index f68394abb3..90a93df880 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/bump-version.md +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/bump-version.md @@ -5,16 +5,16 @@ shortTitle: bump-version weight: 90 --- -When releasing a new version of a nf-core pipeline, version numbers have to be updated in several different places. The helper command `nf-core bump-version` automates this for you to avoid manual errors (and frustration!). +When releasing a new version of a nf-core pipeline, version numbers have to be updated in several different places. The helper command `nf-core pipelines bump-version` automates this for you to avoid manual errors (and frustration!). The command uses results from the linting process, so will only work with workflows that pass these tests. -Usage is `nf-core bump-version `, eg: +Usage is `nf-core pipelines bump-version `, eg: -![`nf-core bump-version 1.1`](/images/tools/nf-core-bump-version.svg) +![`nf-core pipelines bump-version 1.1`](/images/tools/nf-core-bump-version.svg) You can change the directory from the current working directory by specifying `--dir `. To change the required version of Nextflow instead of the pipeline version number, use the flag `--nextflow`. diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/create-logo.md b/sites/docs/src/content/docs/nf-core-tools/pipelines/create-logo.md index 984049f037..71f5a0f1f0 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/create-logo.md +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/create-logo.md @@ -5,12 +5,12 @@ shortTitle: create-logo weight: 110 --- -The `nf-core create-logo` command creates a logo for your pipeline based on the nf-core template and the pipeline name. You can specify the width of the logo in pixels with the `--width` flag. Additionally, you can specify the output format to be either `png` or `svg` with the `--format` flag. The default format is `png`. +The `nf-core pipelines create-logo` command creates a logo for your pipeline based on the nf-core template and the pipeline name. You can specify the width of the logo in pixels with the `--width` flag. Additionally, you can specify the output format to be either `png` or `svg` with the `--format` flag. The default format is `png`. -Usage is `nf-core create-logo `, eg: +Usage is `nf-core pipelines create-logo `, eg: -![`nf-core create-logo nextbigthing`](/images/tools/nf-core-create-logo.svg) +![`nf-core pipelines create-logo nextbigthing`](/images/tools/nf-core-create-logo.svg) diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/create-params-file.md b/sites/docs/src/content/docs/nf-core-tools/pipelines/create-params-file.md index 1d9ca4387d..9d5c4df4d0 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/create-params-file.md +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/create-params-file.md @@ -6,9 +6,9 @@ weight: 30 --- Sometimes it is easier to manually edit a parameter file than to use the web interface or interactive commandline wizard -provided by `nf-core launch`, for example when running a pipeline with many options on a remote server without a graphical interface. +provided by `nf-core pipelines launch`, for example when running a pipeline with many options on a remote server without a graphical interface. -You can create a parameter file with all parameters of a pipeline with the `nf-core create-params-file` command. +You can create a parameter file with all parameters of a pipeline with the `nf-core pipelines create-params-file` command. This file can then be passed to `nextflow` with the `-params-file` flag. This command takes one argument - either the name of a nf-core pipeline which will be pulled automatically, diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/download.md b/sites/docs/src/content/docs/nf-core-tools/pipelines/download.md index fdb6d2709f..16536d2c0b 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/download.md +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/download.md @@ -10,7 +10,7 @@ In this case you will need to fetch the pipeline files first, then manually tran To make this process easier and ensure accurate retrieval of correctly versioned code and software containers, we have written a download helper tool. -The `nf-core download` command will download both the pipeline code and the [institutional nf-core/configs](https://github.com/nf-core/configs) files. It can also optionally download any singularity image files that are required. +The `nf-core pipelines download` command will download both the pipeline code and the [institutional nf-core/configs](https://github.com/nf-core/configs) files. It can also optionally download any singularity image files that are required. If run without any arguments, the download tool will interactively prompt you for the required information. Each option has a flag, if all are supplied then it will run without any user input needed. @@ -19,7 +19,7 @@ Each option has a flag, if all are supplied then it will run without any user in working_dir: tmp --> -![`nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d`](/images/tools/nf-core-download.svg) +![`nf-core pipelines download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d`](/images/tools/nf-core-download.svg) Once downloaded, you will see something like the following file structure for the downloaded pipeline: @@ -48,7 +48,7 @@ So using `-profile ` should work if available within [nf-core/configs](htt ## Downloading Apptainer containers -If you're using [Singularity](https://apptainer.org) (Apptainer), the `nf-core download` command can also fetch the required container images for you. +If you're using [Singularity](https://apptainer.org) (Apptainer), the `nf-core pipelines download` command can also fetch the required container images for you. To do this, select `singularity` in the prompt or specify `--container-system singularity` in the command. Your archive / target output directory will then also include a separate folder `singularity-containers`. @@ -68,9 +68,9 @@ We highly recommend setting the `$NXF_SINGULARITY_CACHEDIR` environment variable If found, the tool will fetch the Singularity images to this directory first before copying to the target output archive / directory. Any images previously fetched will be found there and copied directly - this includes images that may be shared with other pipelines or previous pipeline version downloads or download attempts. -If you are running the download on the same system where you will be running the pipeline (eg. a shared filesystem where Nextflow won't have an internet connection at a later date), you can choose to _only_ use the cache via a prompt or cli options `--container-cache-utilisation amend`. This instructs `nf-core download` to fetch all Singularity images to the `$NXF_SINGULARITY_CACHEDIR` directory but does _not_ copy them to the workflow archive / directory. The workflow config file is _not_ edited. This means that when you later run the workflow, Nextflow will just use the cache folder directly. +If you are running the download on the same system where you will be running the pipeline (eg. a shared filesystem where Nextflow won't have an internet connection at a later date), you can choose to _only_ use the cache via a prompt or cli options `--container-cache-utilisation amend`. This instructs `nf-core pipelines download` to fetch all Singularity images to the `$NXF_SINGULARITY_CACHEDIR` directory but does _not_ copy them to the workflow archive / directory. The workflow config file is _not_ edited. This means that when you later run the workflow, Nextflow will just use the cache folder directly. -If you are downloading a workflow for a different system, you can provide information about the contents of its image cache to `nf-core download`. To avoid unnecessary container image downloads, choose `--container-cache-utilisation remote` and provide a list of already available images as plain text file to `--container-cache-index my_list_of_remotely_available_images.txt`. To generate this list on the remote system, run `find $NXF_SINGULARITY_CACHEDIR -name "*.img" > my_list_of_remotely_available_images.txt`. The tool will then only download and copy images into your output directory, which are missing on the remote system. +If you are downloading a workflow for a different system, you can provide information about the contents of its image cache to `nf-core pipelines download`. To avoid unnecessary container image downloads, choose `--container-cache-utilisation remote` and provide a list of already available images as plain text file to `--container-cache-index my_list_of_remotely_available_images.txt`. To generate this list on the remote system, run `find $NXF_SINGULARITY_CACHEDIR -name "*.img" > my_list_of_remotely_available_images.txt`. The tool will then only download and copy images into your output directory, which are missing on the remote system. ### How the Singularity image downloads work @@ -89,7 +89,7 @@ Once a full list of containers is found, they are processed in the following ord 1. If the target image already exists, nothing is done (eg. with `$NXF_SINGULARITY_CACHEDIR` and `--container-cache-utilisation amend` specified) 2. If found in `$NXF_SINGULARITY_CACHEDIR` and `--container-cache-utilisation copy` is specified, they are copied to the output directory 3. If they start with `http` they are downloaded directly within Python (default 4 at a time, you can customise this with `--parallel-downloads`) -4. If they look like a Docker image name, they are fetched using a `singularity pull` command. Choose the container libraries (registries) queried by providing one or multiple `--container-library` parameter(s). For example, if you call `nf-core download` with `-l quay.io -l ghcr.io -l docker.io`, every image will be pulled from `quay.io` unless an error is encountered. Subsequently, `ghcr.io` and then `docker.io` will be queried for any image that has failed before. +4. If they look like a Docker image name, they are fetched using a `singularity pull` command. Choose the container libraries (registries) queried by providing one or multiple `--container-library` parameter(s). For example, if you call `nf-core pipelines download` with `-l quay.io -l ghcr.io -l docker.io`, every image will be pulled from `quay.io` unless an error is encountered. Subsequently, `ghcr.io` and then `docker.io` will be queried for any image that has failed before. - This requires Singularity/Apptainer to be installed on the system and is substantially slower Note that compressing many GBs of binary files can be slow, so specifying `--compress none` is recommended when downloading Singularity images that are copied to the output directory. diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/launch.md b/sites/docs/src/content/docs/nf-core-tools/pipelines/launch.md index cc9a6dd631..3bff5e8037 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/launch.md +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/launch.md @@ -6,7 +6,7 @@ weight: 20 --- Some nextflow pipelines have a considerable number of command line flags that can be used. -To help with this, you can use the `nf-core launch` command. +To help with this, you can use the `nf-core pipelines launch` command. You can choose between a web-based graphical interface or an interactive command-line wizard tool to enter the pipeline parameters for your run. Both interfaces show documentation alongside each parameter and validate your inputs. @@ -21,7 +21,7 @@ or the path to a directory containing a Nextflow pipeline _(can be any pipeline, -![`nf-core launch rnaseq -r 3.8.1`](/images/tools/nf-core-launch-rnaseq.svg) +![`nf-core pipelines launch rnaseq -r 3.8.1`](/images/tools/nf-core-launch-rnaseq.svg) Once complete, the wizard will ask you if you want to launch the Nextflow run. If not, you can copy and paste the Nextflow command with the `nf-params.json` file of your inputs. diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/licences.md b/sites/docs/src/content/docs/nf-core-tools/pipelines/licences.md index 77e0270206..d08fa3ef83 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/licences.md +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/licences.md @@ -18,4 +18,4 @@ You can use the `licences` subcommand to fetch and print the software licence fr timeout: 10 --> -![`nf-core licences deepvariant`](/images/tools/nf-core-licences.svg) +![`nf-core pipelines licences deepvariant`](/images/tools/nf-core-licences.svg) diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/lint.md b/sites/docs/src/content/docs/nf-core-tools/pipelines/lint.md index 3b84ecd889..90791ae2fa 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/lint.md +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/lint.md @@ -18,9 +18,9 @@ before_command: > fake_command: nf-core lint --> -![`nf-core lint`](/images/tools/nf-core-lint.svg) +![`nf-core pipelines lint`](/images/tools/nf-core-lint.svg) -You can use the `-k` / `--key` flag to run only named tests for faster debugging, eg: `nf-core lint -k files_exist -k files_unchanged`. The `nf-core lint` command lints the current working directory by default, to specify another directory you can use `--dir `. +You can use the `-k` / `--key` flag to run only named tests for faster debugging, eg: `nf-core pipelines lint -k files_exist -k files_unchanged`. The `nf-core pipelines lint` command lints the current working directory by default, to specify another directory you can use `--dir `. ## Linting documentation @@ -56,7 +56,7 @@ lint: - CODE_OF_CONDUCT.md ``` -Note that you have to list all configurations for the `nf-core lint` command under the `lint:` field in the `.nf-core.yml` file, as this file is also used for configuration of other commands. +Note that you have to list all configurations for the `nf-core pipelines lint` command under the `lint:` field in the `.nf-core.yml` file, as this file is also used for configuration of other commands. ## Automatically fix errors @@ -66,5 +66,5 @@ This is so that any automated changes can then be reviewed and undone (`git chec ## Lint results output -The output from `nf-core lint` is designed to be viewed on the command line and is deliberately succinct. +The output from `nf-core pipelines lint` is designed to be viewed on the command line and is deliberately succinct. You can view all passed tests with `--show-passed` or generate JSON / markdown results with the `--json` and `--markdown` flags. diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/list.md b/sites/docs/src/content/docs/nf-core-tools/pipelines/list.md index 5cf877c62b..a1d1ddbb0f 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/list.md +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/list.md @@ -6,17 +6,17 @@ weight: 10 parentWeight: 10 --- -The command `nf-core list` shows all available nf-core pipelines along with their latest version, when that was published and how recently the pipeline code was pulled to your local system (if at all). +The command `nf-core pipelines list` shows all available nf-core pipelines along with their latest version, when that was published and how recently the pipeline code was pulled to your local system (if at all). An example of the output from the command is as follows: -![`nf-core list`](/images/tools/nf-core-list.svg) +![`nf-core pipelines list`](/images/tools/nf-core-list.svg) To narrow down the list, supply one or more additional keywords to filter the pipelines based on matches in titles, descriptions and topics: -![`nf-core list rna rna-seq`](/images/tools/nf-core-list-rna.svg) +![`nf-core pipelines list rna rna-seq`](/images/tools/nf-core-list-rna.svg) You can sort the results by latest release (`-s release`, default), when you last pulled a local copy (`-s pulled`), @@ -25,7 +25,7 @@ or number of GitHub stars (`-s stars`). -![`nf-core list -s stars`](/images/tools/nf-core-list-stars.svg) +![`nf-core pipelines list -s stars`](/images/tools/nf-core-list-stars.svg) To return results as JSON output for downstream use, use the `--json` flag. diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/schema.md b/sites/docs/src/content/docs/nf-core-tools/pipelines/schema.md index 233045a461..1905df4e44 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/schema.md +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/schema.md @@ -11,17 +11,17 @@ Pipeline schema files are built according to the [JSONSchema specification](http To help developers working with pipeline schema, nf-core tools has three `schema` sub-commands: -- `nf-core schema validate` -- `nf-core schema build` -- `nf-core schema docs` -- `nf-core schema lint` +- `nf-core pipelines schema validate` +- `nf-core pipelines schema build` +- `nf-core pipelines schema docs` +- `nf-core pipelines schema lint` ## Validate pipeline parameters Nextflow can take input parameters in a JSON or YAML file when running a pipeline using the `-params-file` option. This command validates such a file against the pipeline schema. -Usage is `nf-core schema validate `. eg with the pipeline downloaded [above](#download-pipeline), you can run: +Usage is `nf-core pipelines schema validate `. eg with the pipeline downloaded [above](#download-pipeline), you can run: -![`nf-core schema validate nf-core-rnaseq/3_8 nf-params.json`](/images/tools/nf-core-schema-validate.svg) +![`nf-core pipelines schema validate nf-core-rnaseq/3_8 nf-params.json`](/images/tools/nf-core-schema-validate.svg) The `pipeline` option can be a directory containing a pipeline, a path to a schema file or the name of an nf-core pipeline (which will be downloaded using `nextflow pull`). ## Build a pipeline schema Manually building JSONSchema documents is not trivial and can be very error prone. -Instead, the `nf-core schema build` command collects your pipeline parameters and gives interactive prompts about any missing or unexpected params. +Instead, the `nf-core pipelines schema build` command collects your pipeline parameters and gives interactive prompts about any missing or unexpected params. If no existing schema is found it will create one for you. Once built, the tool can send the schema to the nf-core website so that you can use a graphical interface to organise and fill in the schema. @@ -51,7 +51,7 @@ timeout: 10 before_command: sed '25,30d' nextflow_schema.json > nextflow_schema.json.tmp && mv nextflow_schema.json.tmp nextflow_schema.json --> -![`nf-core schema build --no-prompts`](/images/tools/nf-core-schema-build.svg) +![`nf-core pipelines schema build --no-prompts`](/images/tools/nf-core-schema-build.svg) There are four flags that you can use with this command: @@ -62,7 +62,7 @@ There are four flags that you can use with this command: ## Display the documentation for a pipeline schema -To get an impression about the current pipeline schema you can display the content of the `nextflow_schema.json` with `nf-core schema docs `. This will print the content of your schema in Markdown format to the standard output. +To get an impression about the current pipeline schema you can display the content of the `nextflow_schema.json` with `nf-core pipelines schema docs `. This will print the content of your schema in Markdown format to the standard output. There are four flags that you can use with this command: @@ -73,7 +73,7 @@ There are four flags that you can use with this command: ## Add new parameters to the pipeline schema -If you want to add a parameter to the schema, you first have to add the parameter and its default value to the `nextflow.config` file with the `params` scope. Afterwards, you run the command `nf-core schema build` to add the parameters to your schema and open the graphical interface to easily modify the schema. +If you want to add a parameter to the schema, you first have to add the parameter and its default value to the `nextflow.config` file with the `params` scope. Afterwards, you run the command `nf-core pipelines schema build` to add the parameters to your schema and open the graphical interface to easily modify the schema. The graphical interface is oganzised in groups and within the groups the single parameters are stored. For a better overview you can collapse all groups with the `Collapse groups` button, then your new parameters will be the only remaining one at the bottom of the page. Now you can either create a new group with the `Add group` button or drag and drop the paramters in an existing group. Therefor the group has to be expanded. The group title will be displayed, if you run your pipeline with the `--help` flag and its description apears on the parameter page of your pipeline. @@ -94,17 +94,17 @@ After filling the schema, click on the `Finished` button in the top right corner ## Update existing pipeline schema -It's important to change the default value of a parameter in the `nextflow.config` file first and then in the pipeline schema, because the value in the config file overwrites the value in the pipeline schema. To change any other parameter use `nf-core schema build --web-only` to open the graphical interface without rebuilding the pipeline schema. Now, the parameters can be changed as mentioned above but keep in mind that changing the parameter datatype depends on the default value specified in the `nextflow.config` file. +It's important to change the default value of a parameter in the `nextflow.config` file first and then in the pipeline schema, because the value in the config file overwrites the value in the pipeline schema. To change any other parameter use `nf-core pipelines schema build --web-only` to open the graphical interface without rebuilding the pipeline schema. Now, the parameters can be changed as mentioned above but keep in mind that changing the parameter datatype depends on the default value specified in the `nextflow.config` file. ## Linting a pipeline schema -The pipeline schema is linted as part of the main pipeline `nf-core lint` command, +The pipeline schema is linted as part of the main pipeline `nf-core pipelines lint` command, however sometimes it can be useful to quickly check the syntax of the JSONSchema without running a full lint run. -Usage is `nf-core schema lint ` (defaulting to `nextflow_schema.json`), eg: +Usage is `nf-core pipelines schema lint ` (defaulting to `nextflow_schema.json`), eg: -![`nf-core schema lint`](/images/tools/nf-core-schema-lint.svg) +![`nf-core pipelines schema lint`](/images/tools/nf-core-schema-lint.svg) diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/sync.md b/sites/docs/src/content/docs/nf-core-tools/pipelines/sync.md index b1abf455c7..449389cfb9 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/sync.md +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/sync.md @@ -15,18 +15,18 @@ Note that pipeline synchronisation happens automatically each time nf-core/tools **As such, you do not normally need to run this command yourself!** This command takes a pipeline directory and attempts to run this synchronisation. -Usage is `nf-core sync`, eg: +Usage is `nf-core pipelines sync`, eg: -![`nf-core sync`](/images/tools/nf-core-sync.svg) +![`nf-core pipelines sync`](/images/tools/nf-core-sync.svg) The sync command tries to check out the `TEMPLATE` branch from the `origin` remote or an existing local branch called `TEMPLATE`. It will fail if it cannot do either of these things. -The `nf-core create` command should make this template automatically when you first start your pipeline. +The `nf-core pipelines create` command should make this template automatically when you first start your pipeline. Please see the [nf-core website sync documentation](https://nf-co.re/developers/sync) if you have difficulties. To specify a directory to sync other than the current working directory, use the `--dir `. diff --git a/sites/docs/src/content/docs/tutorials/adding_a_pipeline/creating_a_pipeline.md b/sites/docs/src/content/docs/tutorials/adding_a_pipeline/creating_a_pipeline.md index 0069a05e40..7da13e8510 100644 --- a/sites/docs/src/content/docs/tutorials/adding_a_pipeline/creating_a_pipeline.md +++ b/sites/docs/src/content/docs/tutorials/adding_a_pipeline/creating_a_pipeline.md @@ -32,7 +32,7 @@ This way we avoid having a lot of "empty" pipelines listed which are basically j See [Adding your pipeline to the nf-core organisation](/docs/tutorials/adding_a_pipeline/move_to_nf-core_org) for details on this process. All nf-core pipelines [_must_ use the nf-core template](/docs/guidelines/pipelines/requirements/use_the_template). -This is done by using the `nf-core create` command - see [the docs](/docs/nf-core-tools/pipelines/create) for detailed instructions. +This is done by using the `nf-core pipelines create` command - see [the docs](/docs/nf-core-tools/pipelines/create) for detailed instructions. This tool does lots of things for you: it gives you the correct file structure and boiler plate code and also sets up the required `git` infrastructure for you to keep your pipeline in sync in the future. @@ -57,7 +57,7 @@ Make sure _not_ to initialise it with _any_ file, `README` or `LICENSE`: you jus You already have these files generated from the nf-core template. Once created, copy the git URL and add this as a remote to your local git repository. -The `nf-core create` command will have initialised a git repository for you, +The `nf-core pipelines create` command will have initialised a git repository for you, so all you need to do is add the remote: ```bash @@ -84,7 +84,7 @@ You can now start writing code for real. Follow usual git development practices, working on the `dev` branch and committing + pushing code as normal. -Remember to run the `nf-core lint` command (see [docs](/docs/nf-core-tools/pipelines/lint)) +Remember to run the `nf-core pipelines lint` command (see [docs](/docs/nf-core-tools/pipelines/lint)) to make sure that your workflow passes all of the nf-core compatibility tests. The automated tests on Github Actions also run this, so you should get a notification from GitHub if something breaks. diff --git a/sites/docs/src/content/docs/tutorials/adding_a_pipeline/first_release.md b/sites/docs/src/content/docs/tutorials/adding_a_pipeline/first_release.md index 82c8bb20c9..0771e9536a 100644 --- a/sites/docs/src/content/docs/tutorials/adding_a_pipeline/first_release.md +++ b/sites/docs/src/content/docs/tutorials/adding_a_pipeline/first_release.md @@ -14,7 +14,7 @@ When the code is stable and ready for a release, set the default branch to `mast ## Bump the version -Use `nf-core bump-version` to increment the version number on the `dev` branch to remove +Use `nf-core pipelines bump-version` to increment the version number on the `dev` branch to remove the `dev` suffix. When developing the pipeline, the version numbers should be numeric with `dev` at the end, @@ -22,13 +22,13 @@ e.g. `0.0.0dev`. When making a release, version numbers should all be numeric. P release numbers MUST use [Semantic Versioning](https://semver.org/). :::tip -Instead of manually changing the version number, use the `nf-core bump-version` command to increment the version numbers. The version number +Instead of manually changing the version number, use the `nf-core pipelines bump-version` command to increment the version numbers. The version number exists in many places in the codebase, and this tool consistently updates all of them. ::: ## Lint the pipeline -Use `nf-core lint --release`. This will check that your code conforms to nf-core expectations. +Use `nf-core pipelines lint --release`. This will check that your code conforms to nf-core expectations. ## Core pipeline review @@ -88,7 +88,7 @@ against the `dev` branch on the nf-core repository. Now that we have a stable `m there should be reviews of each PR against `dev` before merging. When ready to make new releases, make sure that the version number is increased with -`nf-core bump-version` and create a pull-request against `master`. If tests pass, it +`nf-core pipelines bump-version` and create a pull-request against `master`. If tests pass, it can be merged and a new release made. The `master` branch should always have only the commit from the latest release. This is important diff --git a/sites/docs/src/content/docs/tutorials/contributing_to_nf-core/contributing_to_pipelines.md b/sites/docs/src/content/docs/tutorials/contributing_to_nf-core/contributing_to_pipelines.md index c622c6456a..19c205349d 100644 --- a/sites/docs/src/content/docs/tutorials/contributing_to_nf-core/contributing_to_pipelines.md +++ b/sites/docs/src/content/docs/tutorials/contributing_to_nf-core/contributing_to_pipelines.md @@ -41,7 +41,7 @@ If you'd like to write some code for an nf-core pipeline, the standard workflow 1. Check that there isn't already an issue about your idea for that pipeline to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the pipeline repository to your GitHub account 3. Make the necessary changes / additions on `dev` branch by using [git checkout](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/committing-changes-to-a-pull-request-branch-created-from-a-fork) within your forked repository following [pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're new to working with git, you can view the [GitHub pull requests documentation](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or other [excellent `git` resources](https://try.github.io/) to get started. @@ -59,7 +59,7 @@ There are typically two types of tests that run: #### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool that runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool that runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. @@ -96,7 +96,7 @@ If you wish to contribute a new step, please use the following coding standards: 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. @@ -107,7 +107,7 @@ If you wish to contribute a new step, please use the following coding standards: Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. +Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. #### Default processes resource requirements @@ -124,7 +124,7 @@ Please use the following naming schemes, to make it easy to understand what is g #### Nextflow version bumping -If you are using a new feature from core Nextflow, you may bump the minimum required version of Nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` +If you are using a new feature from core Nextflow, you may bump the minimum required version of Nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` #### Images and figures diff --git a/sites/docs/src/content/docs/tutorials/nextflow_training/creating_with_nf-core.md b/sites/docs/src/content/docs/tutorials/nextflow_training/creating_with_nf-core.md index a246e2cf35..469953a4aa 100644 --- a/sites/docs/src/content/docs/tutorials/nextflow_training/creating_with_nf-core.md +++ b/sites/docs/src/content/docs/tutorials/nextflow_training/creating_with_nf-core.md @@ -89,7 +89,7 @@ You can try out some commands, for example listing available nf-core pipelines: ![nf-core list](/images/contributing/creating_with_nf_core/nfcore_list.svg) -In this tutorial we will focus on creating a pipeline, but please do look at the functionality that nf-core/tools provides to you as a user - especially `nf-core launch` and `nf-core download`. +In this tutorial we will focus on creating a pipeline, but please do look at the functionality that nf-core/tools provides to you as a user - especially `nf-core pipelines launch` and `nf-core pipelines download`. ## Creating a pipeline @@ -114,7 +114,7 @@ cd nf-core-demo/ ### Pipeline git repo -The `nf-core create` command has made a fully fledged pipeline for you. +The `nf-core pipelines create` command has made a fully fledged pipeline for you. Before getting too carried away looking at all of the files, note that it has also initiated a git repository: ![git status](/images/contributing/creating_with_nf_core/git_status.svg) @@ -165,7 +165,7 @@ Customising the template is part of writing your new pipeline. However, not _all_ files should be edited - indeed, nf-core strives to promote standardisation amongst pipelines. To try to keep pipelines up to date and using the same code where possible, we have an automated code linting tool for nf-core pipelines. -Running `nf-core lint` will run a comprehensive test suite against your pipeline: +Running `nf-core pipelines lint` will run a comprehensive test suite against your pipeline: ```bash cd nf-core-demo/ @@ -193,7 +193,7 @@ nf-core lint Whilst it's helpful to be able to run the nf-core lint tests locally, their real strength is the combination with CI (continuous integration) testing. By default, nf-core pipelines are configured to run CI tests on GitHub every time you push to the repo or open a pull request. -The same `nf-core lint` command runs on your code on the automated machines. +The same `nf-core pipelines lint` command runs on your code on the automated machines. If there are any failures, they will be reported with a ❌ and you will not be able to merge the pull-request until you push more commits that fix those failures. These automated tests allow us to maintain code quality in a scalable and standardised way across the community. @@ -251,7 +251,7 @@ nextflow run nf-core-demo/ -profile test,docker If you peek inside the `nextflow_schema.json` file you will see that it is quite an intimidating thing. The file is large and complex, and very easy to break if edited manually. -Thankfully, we provide a user-friendly tool for editing this file: `nf-core schema build`. +Thankfully, we provide a user-friendly tool for editing this file: `nf-core pipelines schema build`. To see this in action, let's add some new parameters to `nextflow.config`: @@ -264,7 +264,7 @@ params { // rest of the config file.. ``` -Then run `nf-core schema build`: +Then run `nf-core pipelines schema build`: ```bash cd nf-core-demo/ diff --git a/sites/docs/src/content/docs/tutorials/nf-core_contributing_overview.md b/sites/docs/src/content/docs/tutorials/nf-core_contributing_overview.md index 0da5148649..eda4de056f 100644 --- a/sites/docs/src/content/docs/tutorials/nf-core_contributing_overview.md +++ b/sites/docs/src/content/docs/tutorials/nf-core_contributing_overview.md @@ -123,7 +123,7 @@ nf-core --help The heart of _nf-core_ is the standardisation of pipeline code structure. To achieve this, all pipelines adhere to a generalised pipeline template. -The best way to build an _nf-core_ pipeline is to start by using this template via the `nf-core create` command. +The best way to build an _nf-core_ pipeline is to start by using this template via the `nf-core pipelines create` command. This launches an interactive prompt on the command line which asks for things such as pipeline name, a short description and the author's name. These values are then propagated throughout the template files automatically. @@ -137,7 +137,7 @@ Not everything can be completed with a template and all new pipelines will need To make it easier to find these, the _nf-core_ template files have numerous comment lines beginning with `TODO nf-core:`, followed by a description of what should be changed or added. These comment lines can be deleted once the required change has been made. -Most code editors have tools to automatically discover such `TODO` lines and the `nf-core lint` command will flag these. +Most code editors have tools to automatically discover such `TODO` lines and the `nf-core pipelines lint` command will flag these. This makes it simple to systematically work through the new pipeline, editing all files where required. ### Forks, branches and pull-requests @@ -226,7 +226,7 @@ Note that remote URLs cannot be traversed like a regular file system - so glob f ### GitHub Actions workflows The automated tests with GitHub Actions are configured in the `.github/workflows` folder that is generated by the template. -Each file (`branch.yml`, `ci.yml` and `linting.yml`) defines several tests: branch protection, running the pipeline with the test data, linting the code with `nf-core lint`, linting the syntax of all Markdown documentation and linting the syntax of all YAML files. +Each file (`branch.yml`, `ci.yml` and `linting.yml`) defines several tests: branch protection, running the pipeline with the test data, linting the code with `nf-core pipelines lint`, linting the syntax of all Markdown documentation and linting the syntax of all YAML files. #### Branch protection @@ -234,7 +234,7 @@ The `branch.yml` workflow sets the branch protection for the nf-core repository. It is already set up and does not need to be edited. This test will check that pull-requests going to the nf-core repo `master` branch only come from the `dev` or `patch` branches (for releases). In case you want to add branch protection for a repository outside _nf-core_, you can add an extra step to the workflow with that repository name. -You can leave the _nf-core_ branch protection in place so that the `nf-core lint` command does not throw an error - it only runs on nf-core repositories so it should be ignored. +You can leave the _nf-core_ branch protection in place so that the `nf-core pipelines lint` command does not throw an error - it only runs on nf-core repositories so it should be ignored. #### Linting @@ -247,8 +247,8 @@ It will check: - That any Python is correctly formatted using Black. - That general code structure is maintained (e.g. no trailing whitespaces, final newline is present in all files) with [EditorConfig](https://editorconfig.org/). - That the pipeline code follows the nf-core linting rules. - - You can run this manually with the `nf-core lint` command. - - Some of the linting tests can be fixed automatically with the `--fix` subcommand, for example any `files_unchanged` type of error: `nf-core lint --fix files_unchanged`. + - You can run this manually with the `nf-core pipelines lint` command. + - Some of the linting tests can be fixed automatically with the `--fix` subcommand, for example any `files_unchanged` type of error: `nf-core pipelines lint --fix files_unchanged`. > Tip: when using a code editor, some code editor settings might help you solve any code linting errors by linting when saving a file and even fixing the errors directly. You can check out [this documentation](https://nf-co.re/docs/contributing/editor_plugins) on code editor plugins. @@ -314,7 +314,7 @@ It should mostly work out of the box, but it may need some editing from you to c The matrix `nxf_ver` variable sets the `NXF_VER` environment variable twice. This tells GitHub Actions to run the tests twice in parallel - once with the latest version of Nextflow (`NXF_VER=''`) and once with the minimum version supported by the pipeline. -Do not edit this version number manually - it appears in multiple locations through the pipeline code, so it's better to use `nf-core bump-version --nextflow` instead. +Do not edit this version number manually - it appears in multiple locations through the pipeline code, so it's better to use `nf-core pipelines bump-version --nextflow` instead. The provided tests run your pipeline with the `-profile test,docker --outdir ` flags. This may be sufficient for your pipeline. However, if it is possible to run the pipeline with significantly different options (for example, different alignment tools), then it is good to test all of these. @@ -323,7 +323,7 @@ Do not try to add a run for every possible combination of parameters, as this wo ### Exercise 3 (testing pipelines) -- Run `nf-core lint` on your pipeline and make note of any test warnings / failures. +- Run `nf-core pipelines lint` on your pipeline and make note of any test warnings / failures. - Take a look at `conf/test.config` and edit the test data (you can use another dataset on nf-core/test-datasets). - Check that running the pipeline with the test profile passes @@ -404,7 +404,7 @@ You can find instructions for how to do this at [https://nf-co.re/join](https:// Once you're ready to go, you can fork your repository to _nf-core_. A lot of stuff happens automatically when you do this: the website will update itself to include your new pipeline, complete with rendered documentation pages and usage statistics. -Your pipeline will also appear in the `nf-core list` command output and in various other locations. +Your pipeline will also appear in the `nf-core pipelines list` command output and in various other locations. Unfortunately, at the time of writing, the Zenodo (automated DOI assignment for releases) services are not created automatically. These can only be set up by _nf-core_ administrators, so please ask someone to do this for you on Slack. @@ -423,7 +423,7 @@ Your pipeline will come out the other side stronger than ever! ### Making the first release Once the pseudo-PR is approved, you're ready to make the release. -To do this, first bump the pipeline version to a stable tag using `nf-core bump-version`, then open a pull-request from the `dev` branch to `master`. +To do this, first bump the pipeline version to a stable tag using `nf-core pipelines bump-version`, then open a pull-request from the `dev` branch to `master`. Once tests are passing and two _nf-core_ members have approved this PR, it can be merged to `master`. Then a GitHub release is made, using the contents of the changelog as a description. @@ -438,7 +438,7 @@ We have compiled a detailed [release checklist](https://nf-co.re/docs/checklists Over time, new versions of nf-core/tools will be released with changes to the template. In order to keep all _nf-core_ pipelines in sync, we have developed an automated synchronisation procedure. -A GitHub bot account, [@nf-core-bot](https://github.com/nf-core-bot) is scripted on a new tools release to use `nf-core create` with the new template using the input values you used on your pipeline. +A GitHub bot account, [@nf-core-bot](https://github.com/nf-core-bot) is scripted on a new tools release to use `nf-core pipelines create` with the new template using the input values you used on your pipeline. This is committed to the `TEMPLATE` branch and a pull-request created to incorporate these changes into `dev`. Note that these PRs can sometimes create git _merge conflicts_ which will need to be resolved manually. @@ -447,7 +447,7 @@ Once resolved and checked, this PR can be merged and a new pipeline release crea ### Exercise 5 (releasing pipelines) -- Use `nf-core bump-version --nextflow` to update the required version of Nextflow in your pipeline +- Use `nf-core pipelines bump-version --nextflow` to update the required version of Nextflow in your pipeline - Bump your pipeline's version to 1.0, ready for its first release! - Make sure that you're signed up to the _nf-core_ slack (get an invite on [nf-co.re](https://nf-co.re)) and drop us a line about your latest and greatest pipeline plans! - Ask to be a member of the _nf-core_ GitHub organisation by commenting on [this GitHub issue](https://github.com/nf-core/website/issues/3) diff --git a/sites/docs/src/content/docs/tutorials/sync/fixing_broken_template_branch.md b/sites/docs/src/content/docs/tutorials/sync/fixing_broken_template_branch.md index 12d2bb5e9d..9f18e23079 100644 --- a/sites/docs/src/content/docs/tutorials/sync/fixing_broken_template_branch.md +++ b/sites/docs/src/content/docs/tutorials/sync/fixing_broken_template_branch.md @@ -17,7 +17,7 @@ If so, the easiest solution is to start your `TEMPLATE` branch from scratch. cd ``` -- Next, retrieve the commit hash when the original nf-core template was used to generate pipeline i.e. with `nf-core create`. +- Next, retrieve the commit hash when the original nf-core template was used to generate pipeline i.e. with `nf-core pipelines create`. - Assuming you originally started with the nf-core template, you can simply look at your git log from within your repository: @@ -47,7 +47,7 @@ If so, the easiest solution is to start your `TEMPLATE` branch from scratch. You are irreversibly overwriting git history here - make sure that you get the branch names right! ::: -- We can switch back to `dev`, and run `nf-core sync` to do it's magic and get the latest version of the template. +- We can switch back to `dev`, and run `nf-core pipelines sync` to do it's magic and get the latest version of the template. ```bash git checkout dev diff --git a/sites/docs/src/content/docs/tutorials/sync/manual_sync.md b/sites/docs/src/content/docs/tutorials/sync/manual_sync.md index 711ff92a10..f5ae303825 100644 --- a/sites/docs/src/content/docs/tutorials/sync/manual_sync.md +++ b/sites/docs/src/content/docs/tutorials/sync/manual_sync.md @@ -6,9 +6,9 @@ subtitle: How to manually synchronise your nf-core pipeline with the latest nf-c There are rare cases, when the synchronisation needs to be triggered manually, i.e. it was not executed during an `nf-core/tools` release on Github, or when you want to perform a targeted sync. -Note that automated PR system is only applicable to official nf-core pipelines, homemade pipelines based on nf-core standards/modules created with `nf-core create` have to be updated following this manual synchronisation procedure. +Note that automated PR system is only applicable to official nf-core pipelines, homemade pipelines based on nf-core standards/modules created with `nf-core pipelines create` have to be updated following this manual synchronisation procedure. -You can do so by running the `nf-core sync` command: +You can do so by running the `nf-core pipelines sync` command: ```bash cd my_pipeline @@ -23,11 +23,11 @@ git remote add upstream https://github.com/nf-core/PIPELINE.git git checkout --track upstream/TEMPLATE ``` -Remember to go back to your `dev` branch as above before running `nf-core sync`. +Remember to go back to your `dev` branch as above before running `nf-core pipelines sync`. Much of the merging process should then be the same as described above with the automated pull requests. -In case of manual synchronisation of a homemade pipeline and if you want to have a PR opened to your `dev` branch, you can use this `nf-core sync` template command: +In case of manual synchronisation of a homemade pipeline and if you want to have a PR opened to your `dev` branch, you can use this `nf-core pipelines sync` template command: ```bash nf-core sync \ diff --git a/sites/docs/src/content/docs/tutorials/sync/overview.md b/sites/docs/src/content/docs/tutorials/sync/overview.md index 204f217bfc..0d922a17b3 100644 --- a/sites/docs/src/content/docs/tutorials/sync/overview.md +++ b/sites/docs/src/content/docs/tutorials/sync/overview.md @@ -18,18 +18,18 @@ There are three topics covered in this documentation page: ### How template synchronisation works -The `nf-core` helper tools have a subcommand for synchronising a pipeline with the nf-core template (`nf-core sync`). +The `nf-core` helper tools have a subcommand for synchronising a pipeline with the nf-core template (`nf-core pipelines sync`). Although this can be run manually, it is usually only used by the GitHub Actions automation: when a new version of `nf-core/tools` is released it runs for all nf-core pipelines and automatically opens pull-requests (PRs) with the necessary changes required to update every pipeline. These pull requests then need to be manually resolved and merged by the pipeline maintainers. Behind the scenes, this synchronisation is done by using `git`. -Each repository has a special `TEMPLATE` branch which contains only the "vanilla" code made by the `nf-core create` tool. -The synchronisation tool fetches the essential variables needed to recreate the pipeline and uses this to trigger a `nf-core create --no-git` command with the latest version of the template. +Each repository has a special `TEMPLATE` branch which contains only the "vanilla" code made by the `nf-core pipelines create` tool. +The synchronisation tool fetches the essential variables needed to recreate the pipeline and uses this to trigger a `nf-core pipelines create --no-git` command with the latest version of the template. The result from this is then compared against what is stored in the `TEMPLATE` branch and committed. During an automated sync, a copy of the `TEMPLATE` branch called `nf-core-template-merge-` will be made (to avoid `dev` history to end up in `TEMPLATE` branch after solving merge conflicts), and a PR from this new branch will be opened against your `dev`. When merging from the `nf-core-template-merge-` branch back into the main `dev` branch of the pipeline, `git` should be clever enough to know what has changed since the template was first used, and therefore, it will only present the relevant changes. For this to work in practice, the `TEMPLATE` branch needs to have a shared `git` history with the `master` branch of the pipeline. -The `nf-core create` command initially does this by enforcing a first commit to the `master` branch before any development has taken place. -If the pipeline _was not_ created by the `nf-core create` command, this has to be set up manually. +The `nf-core pipelines create` command initially does this by enforcing a first commit to the `master` branch before any development has taken place. +If the pipeline _was not_ created by the `nf-core pipelines create` command, this has to be set up manually. For instructions on this, see [Setting up a pipeline for syncing retrospectively](#setting-up-a-pipeline-for-syncing-retrospectively). diff --git a/sites/docs/src/content/docs/tutorials/sync/sync_retrospectively.md b/sites/docs/src/content/docs/tutorials/sync/sync_retrospectively.md index 8cca3e1313..d4f82163bf 100644 --- a/sites/docs/src/content/docs/tutorials/sync/sync_retrospectively.md +++ b/sites/docs/src/content/docs/tutorials/sync/sync_retrospectively.md @@ -3,9 +3,9 @@ title: Setting up a pipeline for syncing retrospectively subtitle: How to set up a correct TEMPLATE branch in your nf-core pipeline repository --- -This section describes how to set up a correct TEMPLATE branch in the case your pipeline was not created with a TEMPLATE branch from the beginning. If you created a pipeline with the `nf-core create` command, you should be all ready to go and can skip this step. Otherwise proceed with caution. It is probably a good idea to make sure you have all your local changes pushed to github and you could even make a local backup clone of your repository before proceeding. +This section describes how to set up a correct TEMPLATE branch in the case your pipeline was not created with a TEMPLATE branch from the beginning. If you created a pipeline with the `nf-core pipelines create` command, you should be all ready to go and can skip this step. Otherwise proceed with caution. It is probably a good idea to make sure you have all your local changes pushed to github and you could even make a local backup clone of your repository before proceeding. -You should also consider the option to restart your pipeline project by running the `nf-core create` command and simply copy in the modifications you need into the newly created pipeline. +You should also consider the option to restart your pipeline project by running the `nf-core pipelines create` command and simply copy in the modifications you need into the newly created pipeline. ### Step-by-step procedure diff --git a/sites/docs/src/content/docs/usage/Getting_started/introduction.md b/sites/docs/src/content/docs/usage/Getting_started/introduction.md index 2b709c4b1f..c47e26e05a 100644 --- a/sites/docs/src/content/docs/usage/Getting_started/introduction.md +++ b/sites/docs/src/content/docs/usage/Getting_started/introduction.md @@ -42,7 +42,7 @@ To run a pipeline: nextflow run hello ``` -2. Choose a pipeline to run. See the available [nf-core pipelines](https://nf-co.re/pipelines). If you have [nf-core tools](https://nf-co.re/tools) installed, run `nf-core list`. +2. Choose a pipeline to run. See the available [nf-core pipelines](https://nf-co.re/pipelines). If you have [nf-core tools](https://nf-co.re/tools) installed, run `nf-core pipelines list`. 3. Configure Nextflow to run on your system: diff --git a/sites/docs/src/content/docs/usage/Getting_started/offline.md b/sites/docs/src/content/docs/usage/Getting_started/offline.md index 784ee6090b..d90e86e20c 100644 --- a/sites/docs/src/content/docs/usage/Getting_started/offline.md +++ b/sites/docs/src/content/docs/usage/Getting_started/offline.md @@ -38,7 +38,7 @@ We do this by installing it locally on a machine that _does_ have an internet co To run a pipeline offline, you need the pipeline code, the software dependencies, and the shared nf-core/configs configuration profiles. We have created a helper tool as part of the _nf-core_ package to automate this for you. -On a computer with an internet connection, run `nf-core download ` to download the pipeline and config profiles. +On a computer with an internet connection, run `nf-core pipelines download ` to download the pipeline and config profiles. Add the argument `--container singularity` to also fetch the singularity container(s). The pipeline and requirements will be downloaded, configured with their relative paths, and packaged into a `.tar.gz` file by default. @@ -51,11 +51,11 @@ To run the pipeline, simply use `nextflow run /workflow [pip ### Shared storage -If you are downloading _directly_ to the offline storage (eg. a head node with internet access whilst compute nodes are offline), you can use the `--singularity-cache-only` option for `nf-core download` and set the `$NXF_SINGULARITY_CACHEDIR` environment variable. +If you are downloading _directly_ to the offline storage (eg. a head node with internet access whilst compute nodes are offline), you can use the `--singularity-cache-only` option for `nf-core pipelines download` and set the `$NXF_SINGULARITY_CACHEDIR` environment variable. This downloads the singularity images to the `$NXF_SINGULARITY_CACHEDIR` folder and does not copy them into the target downloaded pipeline folder. This reduces total disk space usage and is faster. -For more information, see the [documentation for `nf-core download`](/docs/nf-core-tools/pipelines/download). +For more information, see the [documentation for `nf-core pipelines download`](/docs/nf-core-tools/pipelines/download). ## Reference genomes From 6c50a170a8eb5a3d25ffecae0d2c1f40a2009a47 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 26 Sep 2024 14:15:04 +0000 Subject: [PATCH 04/35] [automated] Fix code linting --- .../docs/contributing/pipelines/pipeline_file_structure.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sites/docs/src/content/docs/contributing/pipelines/pipeline_file_structure.md b/sites/docs/src/content/docs/contributing/pipelines/pipeline_file_structure.md index 33653ffad1..6dd32229bf 100644 --- a/sites/docs/src/content/docs/contributing/pipelines/pipeline_file_structure.md +++ b/sites/docs/src/content/docs/contributing/pipelines/pipeline_file_structure.md @@ -19,7 +19,7 @@ You will find the following files in each nf-core pipeline. They are automatical | `main.nf` | This is the main nextflow file which will get executed if the pipeline is run. Typically, parameters are initialized and validated in this script before a workflow from the `workflows/` directory is called for execution. | | `nextflow.config` | The main nextflow configuration file. It contains the default pipeline parameters, nextflow configuration options and information like pipeline and minimum nextflow version, among others. The `nextflow.config` also defines different configuration profiles that can be used to run the pipeline. See the [Configuration docs](/docs/usage/getting_started/configuration) for more information. | | `README.md` | Basic information about the pipeline and usage | -| `nextflow_schema.json` | The JSON schema file is used for pipeline parameter specification. This is automatically created using the `nf-core pipelines schema build` command. It is used for printing command-line help, validating input parameters, building the website docs and for building pipeline launch interfaces (web and cli). | +| `nextflow_schema.json` | The JSON schema file is used for pipeline parameter specification. This is automatically created using the `nf-core pipelines schema build` command. It is used for printing command-line help, validating input parameters, building the website docs and for building pipeline launch interfaces (web and cli). | | `CHANGELOG.md` | Information about the changes made to the pipeline for each release. | | `LICENSE` | The license - should be MIT | | `CODE_OF_CONDUCT.md` | The nf-core code of conduct. | From ea4f4aeaf0576fdfba2c178b464097c70f1d6a8e Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 30 Sep 2024 16:26:42 +0200 Subject: [PATCH 05/35] fix Features component --- .../docs/nf-core-tools/pipelines/create.mdx | 27 ++++++++-------- .../pages/docs/nf-core-tools/features.astro | 32 +++++++------------ 2 files changed, 24 insertions(+), 35 deletions(-) diff --git a/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx b/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx index 650bb8e642..30cb3fc7fd 100644 --- a/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx +++ b/sites/docs/src/content/docs/nf-core-tools/pipelines/create.mdx @@ -1,21 +1,18 @@ --- title: Creating a new pipeline -subtitle: Scaffolding a new pipeline using the nf-core template shortTitle: create -weight: 60 -import features from '../../../../pages/docs/nf-core-tools/features.astro' +subtitle: Scaffolding a new pipeline using the nf-core template +weight: 10 --- +import Features from '../../../../pages/docs/nf-core-tools/Features.astro'; + The `create` subcommand makes a new pipeline using the nf-core base template. With a given pipeline name, description and author, it makes a starter pipeline which follows nf-core best practices. 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. - - ![` nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" -a "Big Steve" --plain`](/images/tools/nf-core-create.svg) Once you have run the command, create a new empty repository on GitHub under your username (not the `nf-core` organisation, yet) and push the commits from your computer using the example commands in the above log. @@ -23,19 +20,21 @@ You can then continue to edit, commit and push normally as you build your pipeli Please see the [nf-core documentation](/docs/tutorials/adding_a_pipeline/overview) for a full walkthrough of how to create a new nf-core workflow. -> [!TIP] -> As the command documentation says, remember to come and discuss your idea for a pipeline as early as possible! -> See the [documentation](/docs/tutorials/adding_a_pipeline/move_to_nf-core_org) for instructions. +:::warning +Remember to come and discuss your idea for a pipeline as early as possible! + +See the [documentation](/docs/tutorials/adding_a_pipeline/move_to_nf-core_org) for instructions. +::: -If you prefer, you can supply them as command line arguments. See `nf-core pipelines create --help` for more information. +If you prefer, you can supply the pipeline metadata also as command line arguments. See `nf-core pipelines create --help` for more information. ## Customization The `nf-core pipelines create` command comes with a number of options that allow you to customize the creation of a pipeline. This can be done in two ways: by using the graphical interface, or by supplying a `template.yml` file using the `--template-yaml ` option. Both options allow you to specify a custom pipeline prefix to use instead of the common `nf-core`, as well as selecting parts of the template to be excluded during pipeline creation. -The interface will guide you through the pipeline creation process. Both nf-core and non-nf-core pipelines can be customised, but non-nf-core pipelines have more options which can be skipped. An example of a `template.yml` file is shown below. +The interface will guide you through the pipeline creation process. Both nf-core and non-nf-core pipelines can be customised, but non-nf-core pipelines have more options which can be skipped. See the following example for a `template.yml` file: -```yaml +```yaml title="template.yml" name: coolpipe description: A cool pipeline author: me @@ -82,7 +81,7 @@ This will create a pipeline called `coolpipe` in the directory `myorg-coolpipe` A full list of possible features to skip from the template is described here: - + To run the pipeline creation silently (i.e. without the graphical interface), you can provide all the arguments. The required ones are `--name`, `--description` and `--author`. diff --git a/sites/docs/src/pages/docs/nf-core-tools/features.astro b/sites/docs/src/pages/docs/nf-core-tools/features.astro index a0c5f58f87..2dcc008101 100644 --- a/sites/docs/src/pages/docs/nf-core-tools/features.astro +++ b/sites/docs/src/pages/docs/nf-core-tools/features.astro @@ -1,26 +1,16 @@ --- -import yaml from 'js-yaml'; +import { Markdown } from '@astropub/md'; +import yaml from 'yaml'; -const yamlURL = - 'https://raw.githubusercontent.com/nf-core/tools/refs/heads/dev/nf_core/pipelines/create/template_features.yml'; -const response = await fetch(yamlURL); -const yamlText = await response.text(); -const data = yaml.load(yamlText); +const data = await fetch( + 'https://raw.githubusercontent.com/nf-core/tools/refs/heads/dev/nf_core/pipelines/create/template_features.yml', +) + .then((res) => res.text()) + .then((text) => yaml.parse(text)); -const filteredData = Object.entries(data).map(([key, value]) => { - return { - key, - helpText: value.help_text || 'No help text available', - }; -}); +const markdownContent = Object.entries(data) + .map(([key, value]) => `### \`${key}\`\n\n${value.help_text || 'No help text available'}`) + .join('\n\n'); --- -
    - { - filteredData.map(({ key, helpText }) => ( -
  • - {key}: {helpText} -
    • - )) - } -
+ From b05c04d5b9cb918847068161ad3565854ffc3f9d Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 30 Sep 2024 16:30:00 +0200 Subject: [PATCH 06/35] add/update deps --- package-lock.json | 10550 +++++++++++++++------------------ sites/docs/package.json | 21 +- sites/main-site/package.json | 2 +- 3 files changed, 4921 insertions(+), 5652 deletions(-) diff --git a/package-lock.json b/package-lock.json index 96d1caab71..a244bd4882 100644 --- a/package-lock.json +++ b/package-lock.json @@ -199,12 +199,13 @@ } }, "node_modules/@antfu/install-pkg": { - "version": "0.1.1", - "resolved": "https://registry.npmjs.org/@antfu/install-pkg/-/install-pkg-0.1.1.tgz", - "integrity": "sha512-LyB/8+bSfa0DFGC06zpCEfs89/XoWZwws5ygEa5D+Xsm3OfI+aXQ86VgVG7Acyef+rSZ5HE7J8rrxzrQeM3PjQ==", + "version": "0.4.1", + "resolved": "https://registry.npmjs.org/@antfu/install-pkg/-/install-pkg-0.4.1.tgz", + "integrity": "sha512-T7yB5QNG29afhWVkVq7XeIMBa5U/vs9mX69YqayXypPRmYzUmzwnYltplHmPtZ4HPCn+sQKeXW8I47wCbuBOjw==", + "license": "MIT", "dependencies": { - "execa": "^5.1.1", - "find-up": "^5.0.0" + "package-manager-detector": "^0.2.0", + "tinyexec": "^0.3.0" }, "funding": { "url": "https://github.com/sponsors/antfu" @@ -265,25 +266,25 @@ } }, "node_modules/@astrojs/mdx": { - "version": "3.1.3", - "resolved": "https://registry.npmjs.org/@astrojs/mdx/-/mdx-3.1.3.tgz", - "integrity": "sha512-hOM4dMM4RfJI254d3p/AnOZuk2VyKszRtuY5FBm+Xc4XdhIpGrR56OXMNEcWchtwz4HQyPe/eJSgvBjSROcQIQ==", + "version": "3.1.7", + "resolved": "https://registry.npmjs.org/@astrojs/mdx/-/mdx-3.1.7.tgz", + "integrity": "sha512-8lGdCt+S0TrZgQpbcP3fQJc4cTeacAirtz9TpAMtHCWrQGW8slKt3WG4/0N+bhZgYRC4h5AT5drzFz+y3wvmsg==", + "license": "MIT", "dependencies": { "@astrojs/markdown-remark": "5.2.0", "@mdx-js/mdx": "^3.0.1", "acorn": "^8.12.1", "es-module-lexer": "^1.5.4", "estree-util-visit": "^2.0.0", - "github-slugger": "^2.0.0", "gray-matter": "^4.0.3", - "hast-util-to-html": "^9.0.1", + "hast-util-to-html": "^9.0.2", "kleur": "^4.1.5", "rehype-raw": "^7.0.0", "remark-gfm": "^4.0.0", "remark-smartypants": "^3.0.2", "source-map": "^0.7.4", "unist-util-visit": "^5.0.0", - "vfile": "^6.0.2" + "vfile": "^6.0.3" }, "engines": { "node": "^18.17.1 || ^20.3.0 || >=21.0.0" @@ -293,15 +294,17 @@ } }, "node_modules/@astrojs/netlify": { - "version": "5.4.0", - "resolved": "https://registry.npmjs.org/@astrojs/netlify/-/netlify-5.4.0.tgz", - "integrity": "sha512-zaV/jV4Dm93oahh/Xneh2pOBKOiiFRGpRWwFvH+rkIUR52lfwIWZhngDPxKSKm6TzUd/7vhdba96sEU6cmkxWQ==", + "version": "5.5.3", + "resolved": "https://registry.npmjs.org/@astrojs/netlify/-/netlify-5.5.3.tgz", + "integrity": "sha512-MDbbJY/Qp02WY9TFusXGA9TFSfaRwc/nlyYhk0YZ2ll2KW2DKrXLCJLC17kdhGqKDyg6w4P6juOOgbcGEpfaUw==", + "license": "MIT", "dependencies": { "@astrojs/internal-helpers": "0.4.1", "@astrojs/underscore-redirects": "^0.3.4", "@netlify/functions": "^2.8.0", - "@vercel/nft": "^0.27.2", - "esbuild": "^0.22.0" + "@vercel/nft": "^0.27.4", + "esbuild": "^0.21.5", + "vite": "^5.4.2" }, "peerDependencies": { "astro": "^4.2.0" @@ -397,6 +400,7 @@ "version": "5.2.0", "resolved": "https://registry.npmjs.org/@aws-crypto/crc32/-/crc32-5.2.0.tgz", "integrity": "sha512-nLbCWqQNgUiwwtFsen1AdzAtvuLRsQS8rYgMuxCrdKf9kOssamGLuPwyTY9wyYblNr9+1XM8v6zoDTPPSIeANg==", + "license": "Apache-2.0", "dependencies": { "@aws-crypto/util": "^5.2.0", "@aws-sdk/types": "^3.222.0", @@ -410,6 +414,7 @@ "version": "5.2.0", "resolved": "https://registry.npmjs.org/@aws-crypto/crc32c/-/crc32c-5.2.0.tgz", "integrity": "sha512-+iWb8qaHLYKrNvGRbiYRHSdKRWhto5XlZUEBwDjYNf+ly5SVYG6zEoYIdxvf5R3zyeP16w4PLBn3rH1xc74Rag==", + "license": "Apache-2.0", "dependencies": { "@aws-crypto/util": "^5.2.0", "@aws-sdk/types": "^3.222.0", @@ -468,6 +473,7 @@ "version": "5.2.0", "resolved": "https://registry.npmjs.org/@aws-crypto/sha256-browser/-/sha256-browser-5.2.0.tgz", "integrity": "sha512-AXfN/lGotSQwu6HNcEsIASo7kWXZ5HYWvfOmSNKDsEqC4OashTp8alTmaz+F7TC2L083SFv5RdB+qU3Vs1kZqw==", + "license": "Apache-2.0", "dependencies": { "@aws-crypto/sha256-js": "^5.2.0", "@aws-crypto/supports-web-crypto": "^5.2.0", @@ -482,6 +488,7 @@ "version": "2.2.0", "resolved": "https://registry.npmjs.org/@smithy/is-array-buffer/-/is-array-buffer-2.2.0.tgz", "integrity": "sha512-GGP3O9QFD24uGeAXYUjwSTXARoqpZykHadOmA8G5vfJPK0/DC67qa//0qvqrJzL1xc8WQWX7/yc7fwudjPHPhA==", + "license": "Apache-2.0", "dependencies": { "tslib": "^2.6.2" }, @@ -493,6 +500,7 @@ "version": "2.2.0", "resolved": "https://registry.npmjs.org/@smithy/util-buffer-from/-/util-buffer-from-2.2.0.tgz", "integrity": "sha512-IJdWBbTcMQ6DA0gdNhh/BwrLkDR+ADW5Kr1aZmd4k3DIF6ezMV4R2NIAmT08wQJ3yUK82thHWmC/TnK/wpMMIA==", + "license": "Apache-2.0", "dependencies": { "@smithy/is-array-buffer": "^2.2.0", "tslib": "^2.6.2" @@ -505,6 +513,7 @@ "version": "2.3.0", "resolved": "https://registry.npmjs.org/@smithy/util-utf8/-/util-utf8-2.3.0.tgz", "integrity": "sha512-R8Rdn8Hy72KKcebgLiv8jQcQkXoLMOGGv5uI1/k0l+snqkOzQ1R0ChUBCxWMlBsFMekWjq0wRudIweFs7sKT5A==", + "license": "Apache-2.0", "dependencies": { "@smithy/util-buffer-from": "^2.2.0", "tslib": "^2.6.2" @@ -517,6 +526,7 @@ "version": "5.2.0", "resolved": "https://registry.npmjs.org/@aws-crypto/sha256-js/-/sha256-js-5.2.0.tgz", "integrity": "sha512-FFQQyu7edu4ufvIZ+OadFpHHOt+eSTBaYaki44c+akjg7qZg9oOQeLlk77F6tSYqjDAFClrHJk9tMf0HdVyOvA==", + "license": "Apache-2.0", "dependencies": { "@aws-crypto/util": "^5.2.0", "@aws-sdk/types": "^3.222.0", @@ -580,67 +590,68 @@ } }, "node_modules/@aws-sdk/client-s3": { - "version": "3.614.0", - "resolved": "https://registry.npmjs.org/@aws-sdk/client-s3/-/client-s3-3.614.0.tgz", - "integrity": "sha512-9BlhfeBegvyjOqHtcr9kvrT80wiy7EVUiqYyTFiiDv/hJIcG88XHQCZdLU7658XBkQ7aFrr5b8rF2HRD1oroxw==", + "version": "3.658.1", + "resolved": "https://registry.npmjs.org/@aws-sdk/client-s3/-/client-s3-3.658.1.tgz", + "integrity": "sha512-rxYW7ONoh1y/SM292jt0TEH+LSiztoPCJxT3gst4S2o/85apFY3RxL8TrhOqzXoIeMu2LNzyN51Zygme6AbQAA==", + "license": "Apache-2.0", "dependencies": { "@aws-crypto/sha1-browser": "5.2.0", "@aws-crypto/sha256-browser": "5.2.0", "@aws-crypto/sha256-js": "5.2.0", - "@aws-sdk/client-sso-oidc": "3.614.0", - "@aws-sdk/client-sts": "3.614.0", - "@aws-sdk/core": "3.614.0", - "@aws-sdk/credential-provider-node": "3.614.0", - "@aws-sdk/middleware-bucket-endpoint": "3.614.0", - "@aws-sdk/middleware-expect-continue": "3.609.0", - "@aws-sdk/middleware-flexible-checksums": "3.614.0", - "@aws-sdk/middleware-host-header": "3.609.0", - "@aws-sdk/middleware-location-constraint": "3.609.0", - "@aws-sdk/middleware-logger": "3.609.0", - "@aws-sdk/middleware-recursion-detection": "3.609.0", - "@aws-sdk/middleware-sdk-s3": "3.614.0", - "@aws-sdk/middleware-signing": "3.609.0", - "@aws-sdk/middleware-ssec": "3.609.0", - "@aws-sdk/middleware-user-agent": "3.614.0", - "@aws-sdk/region-config-resolver": "3.614.0", - "@aws-sdk/signature-v4-multi-region": "3.614.0", - "@aws-sdk/types": "3.609.0", - "@aws-sdk/util-endpoints": "3.614.0", - "@aws-sdk/util-user-agent-browser": "3.609.0", - "@aws-sdk/util-user-agent-node": "3.614.0", - "@aws-sdk/xml-builder": "3.609.0", - "@smithy/config-resolver": "^3.0.5", - "@smithy/core": "^2.2.6", - "@smithy/eventstream-serde-browser": "^3.0.4", - "@smithy/eventstream-serde-config-resolver": "^3.0.3", - "@smithy/eventstream-serde-node": "^3.0.4", - "@smithy/fetch-http-handler": "^3.2.1", - "@smithy/hash-blob-browser": "^3.1.2", - "@smithy/hash-node": "^3.0.3", - "@smithy/hash-stream-node": "^3.1.2", - "@smithy/invalid-dependency": "^3.0.3", - "@smithy/md5-js": "^3.0.3", - 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"integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==" + "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==", + "license": "MIT" }, "node_modules/wide-align/node_modules/string-width": { "version": "4.2.3", "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz", "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==", + "license": "MIT", "dependencies": { "emoji-regex": "^8.0.0", "is-fullwidth-code-point": "^3.0.0", @@ -13390,6 +12655,7 @@ "version": "6.0.1", "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz", "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==", + "license": "MIT", "dependencies": { "ansi-regex": "^5.0.1" }, @@ -13499,9 +12765,10 @@ "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==" }, "node_modules/yaml": { - 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"svelte-fast-marquee": "^0.7.0", + "svelte-fast-marquee": "^0.8.0", "ts-dedent": "^2.2.0", "typescript": "^5.5.3", "unist-util-visit": "^5.0.0", diff --git a/sites/docs/package.json b/sites/docs/package.json index e22d4e8469..d5023d4a32 100644 --- a/sites/docs/package.json +++ b/sites/docs/package.json @@ -14,15 +14,16 @@ "test": "playwright test" }, "dependencies": { - "@astrojs/mdx": "^3.1.3", - "@astrojs/netlify": "^5.4.0", - "@iconify-json/fa": "^1.1.8", - "@iconify-json/fa-brands": "^1.1.8", - "@iconify-json/file-icons": "^1.1.9", - "@iconify-json/logos": "^1.1.43", - "@iconify-json/mdi": "^1.1.67", - "@iconify-json/octicon": "^1.1.56", - "@iconify/utils": "^2.1.25", - "svelte-exmarkdown": "^3.0.5" + "@astrojs/mdx": "^3.1.7", + "@astrojs/netlify": "^5.5.3", + "@iconify-json/fa": "^1.2.0", + "@iconify-json/fa-brands": "^1.2.0", + "@iconify-json/file-icons": "^1.2.0", + "@iconify-json/logos": "^1.2.0", + "@iconify-json/mdi": "^1.2.0", + "@iconify-json/octicon": "^1.2.0", + "@iconify/utils": "^2.1.33", + "svelte-exmarkdown": "^3.0.5", + "yaml": "^2.5.1" } } diff --git a/sites/main-site/package.json b/sites/main-site/package.json index 5209ca685d..f5c6dcc2fe 100644 --- a/sites/main-site/package.json +++ b/sites/main-site/package.json @@ -89,7 +89,7 @@ "svelte": "^4.2.18", "svelte-confetti": "^1.4.0", "svelte-exmarkdown": "^3.0.5", - "svelte-fast-marquee": "^0.7.0", + "svelte-fast-marquee": "^0.8.0", "ts-dedent": "^2.2.0", "typescript": "^5.5.3", "unist-util-visit": "^5.0.0", From 1bd032d6c9cecf17d76e91c5320b80a7145c43f2 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 1 Oct 2024 17:11:33 +0200 Subject: [PATCH 07/35] Add first version of the announcement blog post --- .../src/content/blog/2024/tools-3_0_0.md | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 sites/main-site/src/content/blog/2024/tools-3_0_0.md 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.md new file mode 100644 index 0000000000..089fe1e7fb --- /dev/null +++ b/sites/main-site/src/content/blog/2024/tools-3_0_0.md @@ -0,0 +1,30 @@ +--- +title: 'nf-core/tools - 3.0.0' +subtitle: 'What flavour of the nf-core template do you prefer?' +headerImage: 'https://images.unsplash.com/photo-1583258292688-d0213dc5a3a8' +headerImageAlt: 'Yellow and red apples on black plastic crate' +pubDate: 2024-10-03T12:00:00+01:00 +authors: + - 'mirpedrol' + - 'mashehu' +label: + - 'tools' +--- + +# Highlights + +## ⛓️‍💥 Breaking changes + +- All pipeline commands now need the `pipelines` prefix. For example, `nf-core lint{:bash}` is now `nf-core pipelines lint{:bash}`. This makes the commands more consistent with `nf-core modules{:bash}` and `nf-core subworkflows{:bash}` commands. + +## ✨ New features + +- More customisation for pipeline templates. The template has been divided into features which can be skipped, e.g. you can create a new pipeline without any traces of FastQC in it. You can now strip down the pipeline to the bare minimum and add only the tools you need. For nf-core pipelines we still require some core features (e.g. documentation, CI tests, etc.) to be present, but you can still customise the pipeline to your needs. +- A new Text User Interface app when running nf-core pipelines create to help us guide you through the process better (no worries, you can still use the CLI if you give all values as parameters). + +- nf-validation replaced nf-schema in the pipeline template. +- CI tests now lint with the nf-core tools version matching the template version of the pipeline, to minimise errors in opened PRs with every new tools release. + +## 🫡 Deprecations + +- The `nf-core licences{:bash}` command is deprecated. From f316e1ce1fd19dff42e749bbdb061c2d24936db8 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 3 Oct 2024 09:58:28 +0200 Subject: [PATCH 08/35] update lock file --- package-lock.json | 409 +++++++++++++++++++++++----------------------- 1 file changed, 208 insertions(+), 201 deletions(-) diff --git a/package-lock.json b/package-lock.json index 98b45586c1..cdf321a51c 100644 --- a/package-lock.json +++ b/package-lock.json @@ -749,9 +749,9 @@ } }, "node_modules/@aws-sdk/client-s3": { - "version": "3.662.0", - "resolved": "https://registry.npmjs.org/@aws-sdk/client-s3/-/client-s3-3.662.0.tgz", - "integrity": "sha512-zZ38Bjrtjn/KlYSxfkh6rcHX77nOXVZThIOc/RMnsMAC5qS+LT0ruhbYXG2q1Q7BaQ2QWQMz/0n/czWHRbOkNA==", + "version": "3.663.0", + "resolved": "https://registry.npmjs.org/@aws-sdk/client-s3/-/client-s3-3.663.0.tgz", + "integrity": "sha512-XWoy6wglrxFngdswGbccR7cwmafe3ycx2/vIRDuVnIeSYdj/PgYACBt5JEM5NEzW26kFtlJpeN9hUH1i6tyfuQ==", "license": "Apache-2.0", "dependencies": { "@aws-crypto/sha1-browser": "5.2.0", @@ -1469,12 +1469,12 @@ } }, "node_modules/@babel/code-frame": { - 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"node": ">=4" + "node": ">=6" } }, "node_modules/json5": { @@ -9013,9 +9013,9 @@ } }, "node_modules/mermaid": { - "version": "10.9.1", - "resolved": "https://registry.npmjs.org/mermaid/-/mermaid-10.9.1.tgz", - "integrity": "sha512-Mx45Obds5W1UkW1nv/7dHRsbfMM1aOKA2+Pxs/IGHNonygDHwmng8xTHyS9z4KWVi0rbko8gjiBmuwwXQ7tiNA==", + "version": "10.9.2", + "resolved": "https://registry.npmjs.org/mermaid/-/mermaid-10.9.2.tgz", + "integrity": "sha512-UkZyMSuIYcI1Q0H+2pv/5CiY84sOwQ2XlKoDZMl9Y/MtrLEtxQtyA6LWGkMxnZxj0dJqI+7nw51bYjNnrbdFsQ==", "license": "MIT", "dependencies": { "@braintree/sanitize-url": "^6.0.1", @@ -9027,7 +9027,7 @@ "d3-sankey": "^0.12.3", "dagre-d3-es": "7.0.10", "dayjs": "^1.11.7", - "dompurify": "^3.0.5", + "dompurify": "^3.0.5 <3.1.7", "elkjs": "^0.9.0", "katex": "^0.16.9", "khroma": "^2.0.0", @@ -9069,6 +9069,12 @@ "integrity": "sha512-CmBKiL6NNo/OqgmMn95Fk9Whlp2mtvIv+KNpQKN2F4SjvrEesubTRWGYSg+BnWZOnlCaSTU1sMpsBOzgbYhnsA==", "license": "MIT" }, + "node_modules/mermaid/node_modules/dompurify": { + "version": "3.1.6", + "resolved": "https://registry.npmjs.org/dompurify/-/dompurify-3.1.6.tgz", + "integrity": "sha512-cTOAhc36AalkjtBpfG6O8JimdTMWNXjiePT2xQH/ppBGi/4uIpmj8eKyIkMJErXWARyINV/sB38yf8JCLF5pbQ==", + "license": "(MPL-2.0 OR Apache-2.0)" + }, "node_modules/mermaid/node_modules/mdast-util-from-markdown": { "version": "1.3.1", "resolved": "https://registry.npmjs.org/mdast-util-from-markdown/-/mdast-util-from-markdown-1.3.1.tgz", @@ -11304,9 +11310,9 @@ } }, "node_modules/regex": { - "version": "4.3.2", - "resolved": "https://registry.npmjs.org/regex/-/regex-4.3.2.tgz", - "integrity": "sha512-kK/AA3A9K6q2js89+VMymcboLOlF5lZRCYJv3gzszXFHBr6kO6qLGzbm+UIugBEV8SMMKCTR59txoY6ctRHYVw==", + "version": "4.3.3", + "resolved": "https://registry.npmjs.org/regex/-/regex-4.3.3.tgz", + "integrity": "sha512-r/AadFO7owAq1QJVeZ/nq9jNS1vyZt+6t1p/E59B56Rn2GCya+gr1KSyOzNL/er+r+B7phv5jG2xU2Nz1YkmJg==", "license": "MIT" }, "node_modules/regexp-tree": { @@ -12035,9 +12041,9 @@ "license": "Unlicense" }, "node_modules/rollup": { - "version": "4.23.0", - "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.23.0.tgz", - "integrity": "sha512-vXB4IT9/KLDrS2WRXmY22sVB2wTsTwkpxjB8Q3mnakTENcYw3FRmfdYDy/acNmls+lHmDazgrRjK/yQ6hQAtwA==", + "version": "4.24.0", + "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.24.0.tgz", + "integrity": "sha512-DOmrlGSXNk1DM0ljiQA+i+o0rSLhtii1je5wgk60j49d1jHT5YYttBv1iWOnYSTG+fZZESUOSNiAl89SIet+Cg==", "license": "MIT", "dependencies": { "@types/estree": "1.0.6" @@ -12050,22 +12056,22 @@ "npm": ">=8.0.0" }, "optionalDependencies": { - "@rollup/rollup-android-arm-eabi": "4.23.0", - "@rollup/rollup-android-arm64": "4.23.0", - "@rollup/rollup-darwin-arm64": "4.23.0", - "@rollup/rollup-darwin-x64": "4.23.0", - "@rollup/rollup-linux-arm-gnueabihf": "4.23.0", - "@rollup/rollup-linux-arm-musleabihf": "4.23.0", - "@rollup/rollup-linux-arm64-gnu": "4.23.0", - "@rollup/rollup-linux-arm64-musl": "4.23.0", - "@rollup/rollup-linux-powerpc64le-gnu": "4.23.0", - "@rollup/rollup-linux-riscv64-gnu": "4.23.0", - "@rollup/rollup-linux-s390x-gnu": "4.23.0", - "@rollup/rollup-linux-x64-gnu": "4.23.0", - "@rollup/rollup-linux-x64-musl": "4.23.0", - "@rollup/rollup-win32-arm64-msvc": "4.23.0", - "@rollup/rollup-win32-ia32-msvc": "4.23.0", - "@rollup/rollup-win32-x64-msvc": "4.23.0", + "@rollup/rollup-android-arm-eabi": "4.24.0", + "@rollup/rollup-android-arm64": "4.24.0", + "@rollup/rollup-darwin-arm64": "4.24.0", + "@rollup/rollup-darwin-x64": "4.24.0", + "@rollup/rollup-linux-arm-gnueabihf": "4.24.0", + "@rollup/rollup-linux-arm-musleabihf": "4.24.0", + "@rollup/rollup-linux-arm64-gnu": "4.24.0", + "@rollup/rollup-linux-arm64-musl": "4.24.0", + "@rollup/rollup-linux-powerpc64le-gnu": "4.24.0", + "@rollup/rollup-linux-riscv64-gnu": "4.24.0", + "@rollup/rollup-linux-s390x-gnu": "4.24.0", + "@rollup/rollup-linux-x64-gnu": "4.24.0", + "@rollup/rollup-linux-x64-musl": "4.24.0", + "@rollup/rollup-win32-arm64-msvc": "4.24.0", + "@rollup/rollup-win32-ia32-msvc": "4.24.0", + "@rollup/rollup-win32-x64-msvc": "4.24.0", "fsevents": "~2.3.2" } }, @@ -13638,16 +13644,17 @@ "name": "@nf-co.re/docs", "version": "0.0.1", "dependencies": { - "@astrojs/mdx": "^3.1.3", - "@astrojs/netlify": "^5.4.0", - "@iconify-json/fa": "^1.1.8", - "@iconify-json/fa-brands": "^1.1.8", - "@iconify-json/file-icons": "^1.1.9", - "@iconify-json/logos": "^1.1.43", - "@iconify-json/mdi": "^1.1.67", - "@iconify-json/octicon": "^1.1.56", - "@iconify/utils": "^2.1.25", - "svelte-exmarkdown": "^3.0.5" + "@astrojs/mdx": "^3.1.7", + "@astrojs/netlify": "^5.5.3", + "@iconify-json/fa": "^1.2.0", + "@iconify-json/fa-brands": "^1.2.0", + "@iconify-json/file-icons": "^1.2.0", + "@iconify-json/logos": "^1.2.0", + "@iconify-json/mdi": "^1.2.0", + "@iconify-json/octicon": "^1.2.0", + "@iconify/utils": "^2.1.33", + "svelte-exmarkdown": "^3.0.5", + "yaml": "^2.5.1" } }, "sites/main-site": { From 29e5604767e761c0a7fdc453fb7d2f938421496c Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 3 Oct 2024 17:43:36 +0200 Subject: [PATCH 09/35] start adding merge conflict examples --- .../src/content/blog/2024/tools-3_0_0.md | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) 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.md index 089fe1e7fb..2c0991e911 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.md @@ -28,3 +28,48 @@ label: ## 🫡 Deprecations - The `nf-core licences{:bash}` command is deprecated. + +# Common merge conflicts and how to resolve them + +## `README.md` + +In the `## Credits` section, you might encounter a merge conflict like this: + +```diff +<<<<<<< HEAD +- nf-core/mag was written by [Hadrien Gourlé](https://hadriengourle.com) at [SLU](https://slu.se), [Daniel Straub](https://github.com/d4straub) and - [Sabrina Krakau](https://github.com/skrakau) at the [Quantitative Biology Center (QBiC)](http://qbic.life). [James A. Fellows Yates](https://github.- com/jfy133) and [Maxime Borry](https://github.com/maxibor) at the [Max Planck Institute for Evolutionary Anthropology](https://www.eva.mpg.de) joined in version 2.2.0. +- +- Other code contributors include: +- +- - [Antonia Schuster](https://github.com/AntoniaSchuster) +- - [Alexander Ramos](https://github.com/alxndrdiaz) +- - [Carson Miller](https://github.com/CarsonJM) +- - [Daniel Lundin](https://github.com/erikrikarddaniel) +- - [Danielle Callan](https://github.com/d-callan) +- - [Gregory Sprenger](https://github.com/gregorysprenger) +- - [Jim Downie](https://github.com/prototaxites) +- - [Phil Palmer](https://github.com/PhilPalmer) +- - [@willros](https://github.com/willros) +- +- Long read processing was inspired by [caspargross/HybridAssembly](https://github.com/caspargross/HybridAssembly) written by Caspar Gross [@caspargross](https://github.com/caspargross) +======= ++ nf-core/mag was originally written by Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry. +>>>>>>> TEMPLATE +``` + +just ignore the incoming changes and keep the credits as they are. + +## `.nf-core.yml` + +There might be conflicts due to changed order, renamed and new fields, especially in the `template` section. In general, you can accept all incoming changes. +The following fields were added to the file: + +```yaml +template: + force: false + is_nfcore: true + org: nf-core + outdir: . + skip_features: [] + version: 3.0.0 +``` From cd4c850df448ef94fe6e7cf51b6058a72245df68 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 4 Oct 2024 08:22:15 +0200 Subject: [PATCH 10/35] give author advice --- sites/main-site/src/content/blog/2024/tools-3_0_0.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) 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.md index 2c0991e911..1519c046a4 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.md @@ -57,11 +57,15 @@ In the `## Credits` section, you might encounter a merge conflict like this: >>>>>>> TEMPLATE ``` -just ignore the incoming changes and keep the credits as they are. +### How to resolve + +Double check that all authors are included. +If that is the case, ignore the incoming changes and keep the credits as they are. ## `.nf-core.yml` -There might be conflicts due to changed order, renamed and new fields, especially in the `template` section. In general, you can accept all incoming changes. +There might be conflicts due to changed order, renamed and new fields, especially in the `template` section. +In general, you can accept all incoming changes. The following fields were added to the file: ```yaml From daa327a63c69f3e9a89b4f768dbecff827d4b16f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 4 Oct 2024 11:01:21 +0200 Subject: [PATCH 11/35] explain important template changes --- .../src/content/blog/2024/tools-3_0_0.md | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) 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.md index 1519c046a4..0a1227ba4a 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.md @@ -69,11 +69,54 @@ In general, you can accept all incoming changes. The following fields were added to the file: ```yaml +bump_version: null +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 +update: null ``` + +# Relevant template updates + +## The `check_max()` function has been removed + +The `check_map()` function has been replaced by the core Nextflow funcitonality `resourceLimits`. + +The `resourceLimits` are specified in the `nextflow.config` file, and you can remove all mentions to `check_max()` and the parameters that nf-core was using (`max_cpus`, `max_memory` and `max_time`). +You can find more information in the [Nextflow documentation](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits). + +## The `nf-validation plugin` has been replaced by `nf-schema` + +The `nf-validation` plugin is deprecated and we are now using the new version, the `nf-schema` plugin. + +This plugin uses a new JSON schmea draft (2020-12), and thus there are some changes required in the `nextflow_schema.json` and `asses/schema_input.json` files. You can follow the [migration guide](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/) to see the required changes. + +As part of these change, the validation parameters are also replaced, the following parameters have been removed from `nextflow.config` and `nextflow_schema.json`: + +- validationFailUnrecognisedParams +- validationLenientMode +- validationSchemaIgnoreParams +- validationShowHiddenParams +- validate_params + +Instead, the `validation` scope is used to provide `nf-schema` options. + +Note that the definition of plugins and the use of `validation` scope has been relocated after the `manifest` scome. This is to allow accessing `manifest` variables to customise the help message. + +The use of the new `nf-schema` plugin means that we are also replacing the old `UTILS_NFVALIDATION_PLUGIN` subworkflow by `UTILS_NFSCHEMA_PLUGIN`, and how the input samplesheet is read. Please check [the docs](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/#__tabbed_2_2) to find a description of how to use the new `samplesheetToList()` function. + +# Removing for loops and try/catch blocs from `nextflow.config` + +To prepare for some soon to come Nextflow changes, code has been reduced from config files. + +- Including nf-core configs is not done with a try/catch bloc, and the location these include statements has been moved after defining the profiles. This change is important and it is to make sure that overriding of profiles happens correctly, you can find more information in [this](https://github.com/nextflow-io/nextflow/issues/1792) and [this](https://github.com/nextflow-io/nextflow/issues/5306) Nextflow issue. From 88dff6d3fac0352f6917ab0530ddb0bef6814df9 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 4 Oct 2024 12:06:06 +0200 Subject: [PATCH 12/35] specify how to resolve --- sites/main-site/src/content/blog/2024/tools-3_0_0.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) 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.md index 1519c046a4..3c7c4d2fd0 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.md @@ -65,10 +65,9 @@ If that is the case, ignore the incoming changes and keep the credits as they ar ## `.nf-core.yml` There might be conflicts due to changed order, renamed and new fields, especially in the `template` section. -In general, you can accept all incoming changes. The following fields were added to the file: -```yaml +```yaml title=".nf-core.yml" template: force: false is_nfcore: true @@ -77,3 +76,7 @@ template: skip_features: [] version: 3.0.0 ``` + +### How to resolve + +In general, the incoming changes should have the correct values and structure. Double check for duplicated entries and remove them if necessary. From 01bd22532ffa2af5eab5b1533addcd07b413d7f8 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 4 Oct 2024 17:39:29 +0200 Subject: [PATCH 13/35] add description about step-wise sync --- .../src/content/blog/2024/tools-3_0_0.md | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) 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.md index bb0294c0e3..6726af65c8 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.md @@ -29,6 +29,58 @@ label: - The `nf-core licences{:bash}` command is deprecated. +# Avoiding merge conflicts with the new template customisation + +If you don't use don't use any of the following template features: + +- fastqc +- multiqc +- igenomes +- nf_schema + +you can avoid some merge conflicts with a quick update and an intermediate sync: + +1. update the template to the latest version. + +```bash +nf-core pipelines sync +``` + +1. Pull the updated `.nf-core.yml` file from the TEMPLATE branch. + +```bash +git checkout TEMPLATE -- .nf-core.yml +``` + +1. add `fastqc`, `igenomes` or `nf_schema` to skip_features. + +```yaml title=".nf-core.yml" +template: + skip_features: + - fastqc + - igenomes + - nf_schema +``` + +1. Commit the changes + +```bash +git add .nf-core.yml +git commit -m "Skip fastqc, igenomes and nf_schema" +``` + +1. Sync the pipeline again + +```bash +run nf-core pipelines sync +``` + +1. Now you can merge the new template version with _less_ conflicts. + +```bash +git merge TEMPLATE +``` + # Common merge conflicts and how to resolve them ## `README.md` From f14c592b6039212c2688e25341e1d957a1ed7207 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 09:09:16 +0200 Subject: [PATCH 14/35] clarify some sync steps --- .../src/content/blog/2024/tools-3_0_0.md | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) 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.md index 6726af65c8..50107665ba 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.md @@ -40,6 +40,12 @@ If you don't use don't use any of the following template features: you can avoid some merge conflicts with a quick update and an intermediate sync: +1. start by checking out the `dev` branch. + +```bash +git switch dev +``` + 1. update the template to the latest version. ```bash @@ -69,17 +75,9 @@ git add .nf-core.yml git commit -m "Skip fastqc, igenomes and nf_schema" ``` -1. Sync the pipeline again - -```bash -run nf-core pipelines sync -``` - -1. Now you can merge the new template version with _less_ conflicts. +1. Retrigger the pipeline sync via the [GitHub Actions workflow](https://github.com/nf-core/tools/actions/workflows/sync.yml) -```bash -git merge TEMPLATE -``` +1. Your template update merge should now have fewer conflicts. :tada: # Common merge conflicts and how to resolve them From b8f79581e2e2f2245645c9a64b94d9ec1a2ab09a Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 09:28:17 +0200 Subject: [PATCH 15/35] switch order of sections --- .../src/content/blog/2024/tools-3_0_0.md | 70 +++++++++---------- 1 file changed, 35 insertions(+), 35 deletions(-) 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.md index 50107665ba..05978fc3e1 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.md @@ -79,6 +79,41 @@ git commit -m "Skip fastqc, igenomes and nf_schema" 1. Your template update merge should now have fewer conflicts. :tada: +# Relevant template updates + +## The `check_max()` function has been removed + +The `check_map()` function has been replaced by the core Nextflow funcitonality `resourceLimits`. + +The `resourceLimits` are specified in the `nextflow.config` file, and you can remove all mentions to `check_max()` and the parameters that nf-core was using (`max_cpus`, `max_memory` and `max_time`). +You can find more information in the [Nextflow documentation](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits). + +## The `nf-validation plugin` has been replaced by `nf-schema` + +The `nf-validation` plugin is deprecated and we are now using the new version, the `nf-schema` plugin. + +This plugin uses a new JSON schmea draft (2020-12), and thus there are some changes required in the `nextflow_schema.json` and `asses/schema_input.json` files. You can follow the [migration guide](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/) to see the required changes. + +As part of these change, the validation parameters are also replaced, the following parameters have been removed from `nextflow.config` and `nextflow_schema.json`: + +- validationFailUnrecognisedParams +- validationLenientMode +- validationSchemaIgnoreParams +- validationShowHiddenParams +- validate_params + +Instead, the `validation` scope is used to provide `nf-schema` options. + +Note that the definition of plugins and the use of `validation` scope has been relocated after the `manifest` scome. This is to allow accessing `manifest` variables to customise the help message. + +The use of the new `nf-schema` plugin means that we are also replacing the old `UTILS_NFVALIDATION_PLUGIN` subworkflow by `UTILS_NFSCHEMA_PLUGIN`, and how the input samplesheet is read. Please check [the docs](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/#__tabbed_2_2) to find a description of how to use the new `samplesheetToList()` function. + +# Removing for loops and try/catch blocs from `nextflow.config` + +To prepare for some soon to come Nextflow changes, code has been reduced from config files. + +- Including nf-core configs is not done with a try/catch bloc, and the location these include statements has been moved after defining the profiles. This change is important and it is to make sure that overriding of profiles happens correctly, you can find more information in [this](https://github.com/nextflow-io/nextflow/issues/1792) and [this](https://github.com/nextflow-io/nextflow/issues/5306) Nextflow issue. + # Common merge conflicts and how to resolve them ## `README.md` @@ -134,38 +169,3 @@ template: version: 3.0.0 update: null ``` - -# Relevant template updates - -## The `check_max()` function has been removed - -The `check_map()` function has been replaced by the core Nextflow funcitonality `resourceLimits`. - -The `resourceLimits` are specified in the `nextflow.config` file, and you can remove all mentions to `check_max()` and the parameters that nf-core was using (`max_cpus`, `max_memory` and `max_time`). -You can find more information in the [Nextflow documentation](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits). - -## The `nf-validation plugin` has been replaced by `nf-schema` - -The `nf-validation` plugin is deprecated and we are now using the new version, the `nf-schema` plugin. - -This plugin uses a new JSON schmea draft (2020-12), and thus there are some changes required in the `nextflow_schema.json` and `asses/schema_input.json` files. You can follow the [migration guide](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/) to see the required changes. - -As part of these change, the validation parameters are also replaced, the following parameters have been removed from `nextflow.config` and `nextflow_schema.json`: - -- validationFailUnrecognisedParams -- validationLenientMode -- validationSchemaIgnoreParams -- validationShowHiddenParams -- validate_params - -Instead, the `validation` scope is used to provide `nf-schema` options. - -Note that the definition of plugins and the use of `validation` scope has been relocated after the `manifest` scome. This is to allow accessing `manifest` variables to customise the help message. - -The use of the new `nf-schema` plugin means that we are also replacing the old `UTILS_NFVALIDATION_PLUGIN` subworkflow by `UTILS_NFSCHEMA_PLUGIN`, and how the input samplesheet is read. Please check [the docs](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/#__tabbed_2_2) to find a description of how to use the new `samplesheetToList()` function. - -# Removing for loops and try/catch blocs from `nextflow.config` - -To prepare for some soon to come Nextflow changes, code has been reduced from config files. - -- Including nf-core configs is not done with a try/catch bloc, and the location these include statements has been moved after defining the profiles. This change is important and it is to make sure that overriding of profiles happens correctly, you can find more information in [this](https://github.com/nextflow-io/nextflow/issues/1792) and [this](https://github.com/nextflow-io/nextflow/issues/5306) Nextflow issue. From ef2c930c771e7d71e46e64b74d83140a05bbfb43 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 10:35:31 +0200 Subject: [PATCH 16/35] Standardized heading capitalization, add more merge conflict examples --- .../src/content/blog/2024/tools-3_0_0.md | 130 ++++++++++++------ 1 file changed, 89 insertions(+), 41 deletions(-) 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.md index 05978fc3e1..43682de2e1 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.md @@ -15,50 +15,59 @@ label: ## ⛓️‍💥 Breaking changes -- All pipeline commands now need the `pipelines` prefix. For example, `nf-core lint{:bash}` is now `nf-core pipelines lint{:bash}`. This makes the commands more consistent with `nf-core modules{:bash}` and `nf-core subworkflows{:bash}` commands. +- All pipeline commands now require the `pipelines` prefix. + For example, `nf-core lint{:bash}` is now `nf-core pipelines lint{:bash}`. + This change makes the commands more consistent with `nf-core modules{:bash}` and `nf-core subworkflows{:bash}` commands. +- 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`. ## ✨ New features -- More customisation for pipeline templates. The template has been divided into features which can be skipped, e.g. you can create a new pipeline without any traces of FastQC in it. You can now strip down the pipeline to the bare minimum and add only the tools you need. For nf-core pipelines we still require some core features (e.g. documentation, CI tests, etc.) to be present, but you can still customise the pipeline to your needs. -- A new Text User Interface app when running nf-core pipelines create to help us guide you through the process better (no worries, you can still use the CLI if you give all values as parameters). - -- nf-validation replaced nf-schema in the pipeline template. -- CI tests now lint with the nf-core tools version matching the template version of the pipeline, to minimise errors in opened PRs with every 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). +- nf-validation has replaced nf-schema in the pipeline template +- CI tests now use the nf-core tools version matching the pipeline's template version, reducing errors in PRs with each new tools release ## 🫡 Deprecations - The `nf-core licences{:bash}` command is deprecated. -# Avoiding merge conflicts with the new template customisation +# Avoiding Merge Conflicts with Template Customisation -If you don't use don't use any of the following template features: +If you don't use any of these template features: - fastqc - multiqc - igenomes - nf_schema -you can avoid some merge conflicts with a quick update and an intermediate sync: +you can minimize merge conflicts with a quick update and intermediate sync: -1. start by checking out the `dev` branch. +1. Start by checking out the `dev` branch: ```bash git switch dev ``` -1. update the template to the latest version. +1. Update the template to the latest version: ```bash nf-core pipelines sync ``` -1. Pull the updated `.nf-core.yml` file from the TEMPLATE branch. +1. Pull the updated `.nf-core.yml` file from the TEMPLATE branch: ```bash git checkout TEMPLATE -- .nf-core.yml ``` -1. add `fastqc`, `igenomes` or `nf_schema` to skip_features. +1. Add the features you want to skip to `skip_features`: ```yaml title=".nf-core.yml" template: @@ -68,33 +77,32 @@ template: - nf_schema ``` -1. Commit the changes +1. Commit the changes: ```bash git add .nf-core.yml git commit -m "Skip fastqc, igenomes and nf_schema" ``` -1. Retrigger the pipeline sync via the [GitHub Actions workflow](https://github.com/nf-core/tools/actions/workflows/sync.yml) - -1. Your template update merge should now have fewer conflicts. :tada: +1. Retrigger the pipeline sync via the [GitHub Actions workflow](https://github.com/nf-core/tools/actions/workflows/sync.yml) using the name of your pipeline as the input. +1. Your template update merge should now have fewer conflicts! 🎉 -# Relevant template updates +# Important Template Updates -## The `check_max()` function has been removed +## The `check_max()` Function Has Been Removed -The `check_map()` function has been replaced by the core Nextflow funcitonality `resourceLimits`. +The `check_max()` function has been replaced by core Nextflow functionality called [`resourceLimits`](<](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits)>). -The `resourceLimits` are specified in the `nextflow.config` file, and you can remove all mentions to `check_max()` and the parameters that nf-core was using (`max_cpus`, `max_memory` and `max_time`). -You can find more information in the [Nextflow documentation](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits). +The `resourceLimits` are specified in the `nextflow.config` file. You can remove all references to `check_max()` and its associated parameters (`max_cpus`, `max_memory`, and `max_time`). +For more information, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits). -## The `nf-validation plugin` has been replaced by `nf-schema` +## The nf-validation Plugin Has Been Replaced by nf-schema -The `nf-validation` plugin is deprecated and we are now using the new version, the `nf-schema` plugin. +The `nf-validation` plugin is deprecated in favor of the new `nf-schema` plugin. -This plugin uses a new JSON schmea draft (2020-12), and thus there are some changes required in the `nextflow_schema.json` and `asses/schema_input.json` files. You can follow the [migration guide](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/) to see the required changes. +This plugin uses a new JSON schema draft (2020-12), requiring changes to the `nextflow_schema.json` and `assets/schema_input.json` files. Follow the [migration guide](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/) for required changes. -As part of these change, the validation parameters are also replaced, the following parameters have been removed from `nextflow.config` and `nextflow_schema.json`: +The following validation parameters have been removed from `nextflow.config` and `nextflow_schema.json`: - validationFailUnrecognisedParams - validationLenientMode @@ -102,25 +110,29 @@ As part of these change, the validation parameters are also replaced, the follow - validationShowHiddenParams - validate_params -Instead, the `validation` scope is used to provide `nf-schema` options. +Instead, use the `validation` scope for `nf-schema` options. -Note that the definition of plugins and the use of `validation` scope has been relocated after the `manifest` scome. This is to allow accessing `manifest` variables to customise the help message. +:::note +The plugins definition and `validation` scope have been moved after the `manifest` scope to allow access to `manifest` variables for help message customisation. +::: -The use of the new `nf-schema` plugin means that we are also replacing the old `UTILS_NFVALIDATION_PLUGIN` subworkflow by `UTILS_NFSCHEMA_PLUGIN`, and how the input samplesheet is read. Please check [the docs](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/#__tabbed_2_2) to find a description of how to use the new `samplesheetToList()` function. +The `UTILS_NFVALIDATION_PLUGIN` subworkflow has been replaced by `UTILS_NFSCHEMA_PLUGIN`, changing how the input samplesheet is read. See [the documentation](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/#__tabbed_2_2) for details on using the new `samplesheetToList()` function. -# Removing for loops and try/catch blocs from `nextflow.config` +# Removing for-loops and try/catch Blocks from nextflow.config -To prepare for some soon to come Nextflow changes, code has been reduced from config files. +To prepare for upcoming Nextflow changes, code in config files has been simplified: -- Including nf-core configs is not done with a try/catch bloc, and the location these include statements has been moved after defining the profiles. This change is important and it is to make sure that overriding of profiles happens correctly, you can find more information in [this](https://github.com/nextflow-io/nextflow/issues/1792) and [this](https://github.com/nextflow-io/nextflow/issues/5306) Nextflow issue. +- 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 how to resolve them +# Common Merge Conflicts and Solutions -## `README.md` +## README.md -In the `## Credits` section, you might encounter a merge conflict like this: +In the `## Credits` section, you might see conflicts like this: -```diff +```diff title="README.md" <<<<<<< HEAD - nf-core/mag was written by [Hadrien Gourlé](https://hadriengourle.com) at [SLU](https://slu.se), [Daniel Straub](https://github.com/d4straub) and - [Sabrina Krakau](https://github.com/skrakau) at the [Quantitative Biology Center (QBiC)](http://qbic.life). [James A. Fellows Yates](https://github.- com/jfy133) and [Maxime Borry](https://github.com/maxibor) at the [Max Planck Institute for Evolutionary Anthropology](https://www.eva.mpg.de) joined in version 2.2.0. - @@ -137,22 +149,56 @@ In the `## Credits` section, you might encounter a merge conflict like this: - - [@willros](https://github.com/willros) - - Long read processing was inspired by [caspargross/HybridAssembly](https://github.com/caspargross/HybridAssembly) written by Caspar Gross [@caspargross](https://github.com/caspargross) +- nf-core/mag was written by [Hadrien Gourlé](https://hadriengourle.com) at [SLU](https://slu.se), [Daniel Straub](https://github.com/d4straub) and [Sabrina Krakau](https://github.com/skrakau) at the [Quantitative Biology Center (QBiC)](http://qbic.life). ======= + nf-core/mag was originally written by Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry. >>>>>>> TEMPLATE ``` -### How to resolve +### Resolution + +Verify that all authors are included. If confirmed, keep your existing credits section and ignore incoming changes. + +## `CITATIONS.md` + +Citations you added might have been removed in the template update. + +### Resolution + +Reject the incoming changes to keep your citations. + +## `conf/base.config` + +The above mentioned removal of `check_max()` might cause conflicts in the config files + +```diff title="conf/base.config" +<<<<<<< HEAD +- cpus = { check_max( 1 * task.attempt, 'cpus' ) } +- memory = { check_max( 6.GB * task.attempt, 'memory' ) } +- time = { check_max( 4.h * task.attempt, 'time' ) } +======= ++ // TODO nf-core: Check the defaults for all processes ++ cpus = { 1 * task.attempt } ++ memory = { 6.GB * task.attempt } ++ time = { 4.h * task.attempt } +>>>>>>> TEMPLATE +``` + +### Resolution -Double check that all authors are included. -If that is the case, ignore the incoming changes and keep the credits as they are. +Double-check the values and accept the incoming changes if correct. ## `.nf-core.yml` There might be conflicts due to changed order, renamed and new fields, especially in the `template` section. -The following fields were added to the file: -```yaml +### Resolution + +Double-check the changes for duplicates and accept the incoming changes. + +The new file should follow this structure: + +```yaml title=".nf-core.yml" bump_version: null lint: null nf_core_version: 3.0.0 @@ -169,3 +215,5 @@ template: version: 3.0.0 update: null ``` + +See the [API docs](/docs/nf-core-tools/api_reference/dev/api/utils#pydantic-modelpythonnf_coreutilsnfcoretemplateconfigpython) for a more detailed description of each field and the allowed input values. From c110e2a6012c20aaebe14e07d879ef85312a8a2b Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 11:10:39 +0200 Subject: [PATCH 17/35] fix linting and add `nextflow.config` advice --- sites/main-site/src/content/blog/2024/tools-3_0_0.md | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) 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.md index 43682de2e1..142bd511f6 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.md @@ -31,7 +31,7 @@ label: 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). -- nf-validation has replaced nf-schema in the pipeline template +- [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) has replaced nf-validation in the pipeline template - CI tests now use the nf-core tools version matching the pipeline's template version, reducing errors in PRs with each new tools release ## 🫡 Deprecations @@ -91,7 +91,7 @@ git commit -m "Skip fastqc, igenomes and nf_schema" ## The `check_max()` Function Has Been Removed -The `check_max()` function has been replaced by core Nextflow functionality called [`resourceLimits`](<](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits)>). +The `check_max()` function has been replaced by core Nextflow functionality called [`resourceLimits`](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits). The `resourceLimits` are specified in the `nextflow.config` file. You can remove all references to `check_max()` and its associated parameters (`max_cpus`, `max_memory`, and `max_time`). For more information, see the [Nextflow documentation](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits). @@ -217,3 +217,11 @@ update: null ``` See the [API docs](/docs/nf-core-tools/api_reference/dev/api/utils#pydantic-modelpythonnf_coreutilsnfcoretemplateconfigpython) for a more detailed description of each field and the allowed input values. + +## `nextflow.conifg` + +Several merge conflicts to do changes described in [Important Template Updates](http://localhost:4321/blog/2024/tools-3_0_0#important-template-updates) + +### Resolution + +Double-check in the paramters section, that no pipeline-specific parameter would be removed by the incoming changes. In general, you can accept the incoming changes for this file. From c2cea8cf125fc9b2f0275acd57fdaf10f5734195 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 11:41:07 +0200 Subject: [PATCH 18/35] add ch_samplesheet section --- .../src/content/blog/2024/tools-3_0_0.md | 25 ++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) 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.md index 142bd511f6..c262c26528 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.md @@ -98,7 +98,7 @@ For more information, see the [Nextflow documentation](https://www.nextflow.io/d ## The nf-validation Plugin Has Been Replaced by nf-schema -The `nf-validation` plugin is deprecated in favor of the new `nf-schema` plugin. +The `nf-validation` plugin is deprecated in favour of the new `nf-schema` plugin. This plugin uses a new JSON schema draft (2020-12), requiring changes to the `nextflow_schema.json` and `assets/schema_input.json` files. Follow the [migration guide](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/) for required changes. @@ -225,3 +225,26 @@ Several merge conflicts to do changes described in [Important Template Updates]( ### Resolution Double-check in the paramters section, that no pipeline-specific parameter would be removed by the incoming changes. In general, you can accept the incoming changes for this file. + +## `subworkflows/local/utils_nfcore_$PIPELINE_NAME_pipeline/main.nf` + +The switch to `nf-schema` might cause conflicts in the logic of reading in a samplesheet. + +### Resolution + +Be careful in accepting incoming changes. The main changes you should do are: + +```diff title="subworkflows/local/utils_nfcore_$PIPELINE_NAME_pipeline/main.nf" +- include { fromSamplesheet } from 'plugin/nf-validation' ++ include { samplesheetToList } from 'plugin/nf-schema' +``` + +```diff title="subworkflows/local/utils_nfcore_$PIPELINE_NAME_pipeline/main.nf" +- Channel.fromSamplesheet("input") ++ Channel.fromList(samplesheetToList(params.input, "path/to/samplesheet/schema")) +``` + +```diff title="subworkflows/local/utils_nfcore_$PIPELINE_NAME_pipeline/main.nf" +- UTILS_NFVALIDATION_PLUGIN ( ++ UTILS_NFSCHEMA_PLUGIN ( +``` From ce20c545feb5648bf55d80d1267b5d827401fc29 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 11:46:10 +0200 Subject: [PATCH 19/35] add link to migration guide --- sites/main-site/src/content/blog/2024/tools-3_0_0.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) 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.md index c262c26528..c73ba34a04 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.md @@ -220,11 +220,11 @@ See the [API docs](/docs/nf-core-tools/api_reference/dev/api/utils#pydantic-mode ## `nextflow.conifg` -Several merge conflicts to do changes described in [Important Template Updates](http://localhost:4321/blog/2024/tools-3_0_0#important-template-updates) +Several merge conflicts to do changes described in [Important Template Updates](http://localhost:4321/blog/2024/tools-3_0_0#important-template-updates). ### Resolution -Double-check in the paramters section, that no pipeline-specific parameter would be removed by the incoming changes. In general, you can accept the incoming changes for this file. +Double-check in the parameters section, that no pipeline-specific parameter would be removed by the incoming changes. In general, you can accept the incoming changes for this file. ## `subworkflows/local/utils_nfcore_$PIPELINE_NAME_pipeline/main.nf` @@ -248,3 +248,5 @@ Be careful in accepting incoming changes. The main changes you should do are: - UTILS_NFVALIDATION_PLUGIN ( + UTILS_NFSCHEMA_PLUGIN ( ``` + +See the [nf-schema migration guide](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/) for more details in replacing the `fromSamplesheet` function. From eb7e00e5809783acfebca387c7af0c718743e057 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 14:05:51 +0200 Subject: [PATCH 20/35] first try on an intro paragraph --- .../src/content/blog/2024/tools-3_0_0.md | 48 ++++++++++++------- 1 file changed, 30 insertions(+), 18 deletions(-) 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.md index c73ba34a04..902934bde2 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.md @@ -11,18 +11,15 @@ label: - 'tools' --- -# Highlights +# Previously on nf-core/tools -## ⛓️‍💥 Breaking changes +We released nf-core/tools v2.0 in March 2021, which moved the template and tooling to DSL2 and introduced nf-core/modules commands. In following releases we added subworkflows, switched to using nf-validation for schema validation and removed as much python code as possible from the template. +While this happened the nf-core community grew to now 10,000 slack members including 2,000 active users, who are working on 113 pipelines, 1343 modules and 72 subworkflows. With this growth we also saw new scientific areas being covered by nf-core pipelines, for example imaging data both on a [micro scale](https://nf-co.re/molkart/) and on a [global scale](https://nf-co.re/rangeland/). +This and the adoption of the nf-core template and tooling even outside the nf-core community, convinced us to make the nf-core template even more flexible and to improve the user experience of the nf-core/tools. -- All pipeline commands now require the `pipelines` prefix. - For example, `nf-core lint{:bash}` is now `nf-core pipelines lint{:bash}`. - This change makes the commands more consistent with `nf-core modules{:bash}` and `nf-core subworkflows{:bash}` commands. -- 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`. +# What's new in nf-core/tools v3.0.0 + +No worries, this is not as big of a change as the v2.0 release. The main things are: ## ✨ New features @@ -34,13 +31,28 @@ label: - [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) has replaced nf-validation in the pipeline template - CI tests now use the nf-core tools version matching the pipeline's template version, reducing errors in PRs with each new tools release +## ⛓️‍💥 Breaking changes + +- All pipeline commands now require the `pipelines` prefix. + For example, `nf-core lint{:bash}` is now `nf-core pipelines lint{:bash}`. + This change makes the commands more consistent with `nf-core modules{:bash}` and `nf-core subworkflows{:bash}` commands. +- 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. -# Avoiding Merge Conflicts with Template Customisation +# Tip: Avoiding Merge Conflicts + +The v3 release of nf-core/tools includes the ability to have fine-grained control of which template features to include. +You can use this new functionality to switch off chunks of the template. +Doing so means less code will update in the template, and fewer merge conflicts in files that you don't care about. -If you don't use any of these template features: +So - if you don't use any of these template features: - fastqc - multiqc @@ -55,19 +67,19 @@ you can minimize merge conflicts with a quick update and intermediate sync: git switch dev ``` -1. Update the template to the latest version: +2. Update the template to the latest version: ```bash nf-core pipelines sync ``` -1. Pull the updated `.nf-core.yml` file from the TEMPLATE branch: +3. Pull the updated `.nf-core.yml` file from the TEMPLATE branch: ```bash git checkout TEMPLATE -- .nf-core.yml ``` -1. Add the features you want to skip to `skip_features`: +4. Add the features you want to skip to `skip_features`: ```yaml title=".nf-core.yml" template: @@ -77,15 +89,15 @@ template: - nf_schema ``` -1. Commit the changes: +5. Commit the changes: ```bash git add .nf-core.yml git commit -m "Skip fastqc, igenomes and nf_schema" ``` -1. Retrigger the pipeline sync via the [GitHub Actions workflow](https://github.com/nf-core/tools/actions/workflows/sync.yml) using the name of your pipeline as the input. -1. Your template update merge should now have fewer conflicts! 🎉 +6. Retrigger the pipeline sync via the [GitHub Actions workflow](https://github.com/nf-core/tools/actions/workflows/sync.yml) using the name of your pipeline as the input. +7. Your template update merge should now have fewer conflicts! 🎉 # Important Template Updates From 7f48dbcb4ee84ca690cf31731ae4d32790b7835e Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 7 Oct 2024 14:16:02 +0200 Subject: [PATCH 21/35] break highlits points and list changed commands --- .../src/content/blog/2024/tools-3_0_0.md | 32 ++++++++++++++++++- 1 file changed, 31 insertions(+), 1 deletion(-) 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.md index 902934bde2..b30687398b 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.md @@ -31,11 +31,41 @@ No worries, this is not as big of a change as the v2.0 release. The main things - [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) has replaced nf-validation in the pipeline template - CI tests now use the nf-core tools version matching the pipeline's template version, reducing errors in PRs with each new tools release +## ✨ 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). +- [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) has replaced nf-validation in the pipeline 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. - For example, `nf-core lint{:bash}` is now `nf-core pipelines lint{:bash}`. This change makes the commands more consistent with `nf-core modules{:bash}` and `nf-core subworkflows{:bash}` commands. + The commands which changed are: + + ```bash + nf-core lint -> nf-core pipelines lint + nf-core launch -> nf-core pipelines launch + nf-core download -> nf-core pipelines download + nf-core create-params-file -> nf-core pipelines create-params-file + nf-core create -> nf-core pipelines create + nf-core lint -> nf-core pipelines lint + nf-core bump-version -> nf-core pipelines bump-version + nf-core sync -> nf-core pipelines sync + nf-core schema build -> nf-core pipelines schema build + nf-core schema docs -> nf-core pipelines schema docs + nf-core schema lint -> nf-core pipelines schema lint + nf-core schema validate -> nf-core pipelines schema validate + nf-core create-logo -> nf-core pipelines create-logo + ``` + - 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: From 3854e63b2b95bc3f16b38a3e7a20fa514dae37ed Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 14:18:35 +0200 Subject: [PATCH 22/35] add comparison --- sites/main-site/src/content/blog/2024/tools-3_0_0.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) 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.md index 902934bde2..caa4988c43 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.md @@ -13,8 +13,10 @@ label: # Previously on nf-core/tools -We released nf-core/tools v2.0 in March 2021, which moved the template and tooling to DSL2 and introduced nf-core/modules commands. In following releases we added subworkflows, switched to using nf-validation for schema validation and removed as much python code as possible from the template. -While this happened the nf-core community grew to now 10,000 slack members including 2,000 active users, who are working on 113 pipelines, 1343 modules and 72 subworkflows. With this growth we also saw new scientific areas being covered by nf-core pipelines, for example imaging data both on a [micro scale](https://nf-co.re/molkart/) and on a [global scale](https://nf-co.re/rangeland/). +We released nf-core/tools v2.0 in March 2021, which moved the template and tooling to DSL2 and introduced nf-core/modules commands. +In following releases we added subworkflows, switched to using nf-validation for schema validation and removed as much python code as possible from the template. +While this happened the nf-core community grew to now 10,000 slack members including 2,000 active users, who are working on 113 pipelines (compared to 49 when 2.0 was released), 1343 modules and 72 subworkflows. +With this growth we also saw new scientific areas being covered by nf-core pipelines, for example imaging data both on a [micro scale](https://nf-co.re/molkart/) and on a [global scale](https://nf-co.re/rangeland/). This and the adoption of the nf-core template and tooling even outside the nf-core community, convinced us to make the nf-core template even more flexible and to improve the user experience of the nf-core/tools. # What's new in nf-core/tools v3.0.0 From e0455a824280590b073c131599b507ae9f928b1a Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 14:22:26 +0200 Subject: [PATCH 23/35] make command transition a table for better syntax highilghting --- .../src/content/blog/2024/tools-3_0_0.md | 42 +++++++++---------- 1 file changed, 21 insertions(+), 21 deletions(-) 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.md index a9ff5699ca..f85b95a541 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.md @@ -36,15 +36,15 @@ No worries, this is not as big of a change as the v2.0 release. The main things ## ✨ 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. + 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). + 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). - [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) has replaced nf-validation in the pipeline 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 + This will reduce errors in opened PRs with each new tools release ## ⛓️‍💥 Breaking changes @@ -52,21 +52,21 @@ No worries, this is not as big of a change as the v2.0 release. The main things This change makes the commands more consistent with `nf-core modules{:bash}` and `nf-core subworkflows{:bash}` commands. The commands which changed are: - ```bash - nf-core lint -> nf-core pipelines lint - nf-core launch -> nf-core pipelines launch - nf-core download -> nf-core pipelines download - nf-core create-params-file -> nf-core pipelines create-params-file - nf-core create -> nf-core pipelines create - nf-core lint -> nf-core pipelines lint - nf-core bump-version -> nf-core pipelines bump-version - nf-core sync -> nf-core pipelines sync - nf-core schema build -> nf-core pipelines schema build - nf-core schema docs -> nf-core pipelines schema docs - nf-core schema lint -> nf-core pipelines schema lint - nf-core schema validate -> nf-core pipelines schema validate - nf-core create-logo -> nf-core pipelines create-logo - ``` + | 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`. From 1fa73edfd88552703204635348000ee70b2446e0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 7 Oct 2024 14:24:23 +0200 Subject: [PATCH 24/35] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Phil Ewels Co-authored-by: Júlia Mir Pedrol --- sites/main-site/src/content/blog/2024/tools-3_0_0.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) 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.md index f85b95a541..74c363b792 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.md @@ -25,7 +25,8 @@ No worries, this is not as big of a change as the v2.0 release. The main things ## ✨ New features -- Enhanced pipeline template customisation: The template has been divided into features that can be selectively included or excluded. +- 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. @@ -157,14 +158,14 @@ The following validation parameters have been removed from `nextflow.config` and Instead, use the `validation` scope for `nf-schema` options. :::note -The plugins definition and `validation` scope have been moved after the `manifest` scope to allow access to `manifest` variables for help message customisation. +The plugins definition and `validation` scope have been moved further down `nextflow.config` and are now found after the `manifest` scope. This allows access to `manifest` variables to help improve message customisation. ::: The `UTILS_NFVALIDATION_PLUGIN` subworkflow has been replaced by `UTILS_NFSCHEMA_PLUGIN`, changing how the input samplesheet is read. See [the documentation](https://nextflow-io.github.io/nf-schema/2.0/migration_guide/#__tabbed_2_2) for details on using the new `samplesheetToList()` function. -# Removing for-loops and try/catch Blocks from nextflow.config +# Removing scripting from `nextflow.config` -To prepare for upcoming Nextflow changes, code in config files has been simplified: +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 @@ -264,7 +265,7 @@ See the [API docs](/docs/nf-core-tools/api_reference/dev/api/utils#pydantic-mode ## `nextflow.conifg` -Several merge conflicts to do changes described in [Important Template Updates](http://localhost:4321/blog/2024/tools-3_0_0#important-template-updates). +Several merge conflicts due to changes described in [Important Template Updates](http://localhost:4321/blog/2024/tools-3_0_0#important-template-updates). ### Resolution From 03ab45f44394963596cfae0f97a09fce8522ff24 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 14:25:39 +0200 Subject: [PATCH 25/35] update frontmatter --- .../src/content/blog/2024/tools-3_0_0.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) 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.md index f85b95a541..774bb03cfd 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.md @@ -2,11 +2,12 @@ title: 'nf-core/tools - 3.0.0' subtitle: 'What flavour of the nf-core template do you prefer?' headerImage: 'https://images.unsplash.com/photo-1583258292688-d0213dc5a3a8' -headerImageAlt: 'Yellow and red apples on black plastic crate' -pubDate: 2024-10-03T12:00:00+01:00 +headerImageAlt: 'Shelves of yellow and red apples on display in a supermarket' +pubDate: 2024-10-07T14:00:00+01:00 authors: - 'mirpedrol' - 'mashehu' + - 'ewels' label: - 'tools' --- @@ -148,11 +149,11 @@ 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. From 18790b34db19f7f3448bfb02e35529e0119d777c Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 14:31:08 +0200 Subject: [PATCH 26/35] hide too deep headings --- .../src/content/blog/2024/tools-3_0_0.md | 25 ++++++++++--------- sites/main-site/src/content/config.ts | 1 + .../src/pages/blog/[...blogpost].astro | 1 + 3 files changed, 15 insertions(+), 12 deletions(-) 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.md index 5294d3f826..92207b66c6 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.md @@ -10,6 +10,7 @@ authors: - 'ewels' label: - 'tools' +maxHeadingDepth: 3 --- # Previously on nf-core/tools @@ -27,10 +28,10 @@ No worries, this is not as big of a change as the v2.0 release. The main things ## ✨ 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. + - 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). - [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) has replaced nf-validation in the pipeline template - CI tests now use the nf-core tools version matching the pipeline's template version, reducing errors in PRs with each new tools release @@ -174,9 +175,9 @@ To prepare for upcoming Nextflow syntax depreciations, for loops and try/catch b # Common Merge Conflicts and Solutions -## README.md +## `README.md` -In the `## Credits` section, you might see conflicts like this: +In the `## Credits{:md}` section, you might see conflicts like this: ```diff title="README.md" <<<<<<< HEAD @@ -201,7 +202,7 @@ In the `## Credits` section, you might see conflicts like this: >>>>>>> TEMPLATE ``` -### Resolution +#### Resolution Verify that all authors are included. If confirmed, keep your existing credits section and ignore incoming changes. @@ -209,7 +210,7 @@ Verify that all authors are included. If confirmed, keep your existing credits s Citations you added might have been removed in the template update. -### Resolution +#### Resolution Reject the incoming changes to keep your citations. @@ -230,7 +231,7 @@ The above mentioned removal of `check_max()` might cause conflicts in the config >>>>>>> TEMPLATE ``` -### Resolution +#### Resolution Double-check the values and accept the incoming changes if correct. @@ -238,7 +239,7 @@ Double-check the values and accept the incoming changes if correct. There might be conflicts due to changed order, renamed and new fields, especially in the `template` section. -### Resolution +#### Resolution Double-check the changes for duplicates and accept the incoming changes. @@ -268,7 +269,7 @@ See the [API docs](/docs/nf-core-tools/api_reference/dev/api/utils#pydantic-mode Several merge conflicts due to changes described in [Important Template Updates](http://localhost:4321/blog/2024/tools-3_0_0#important-template-updates). -### Resolution +#### Resolution Double-check in the parameters section, that no pipeline-specific parameter would be removed by the incoming changes. In general, you can accept the incoming changes for this file. @@ -276,7 +277,7 @@ Double-check in the parameters section, that no pipeline-specific parameter woul The switch to `nf-schema` might cause conflicts in the logic of reading in a samplesheet. -### Resolution +#### Resolution Be careful in accepting incoming changes. The main changes you should do are: diff --git a/sites/main-site/src/content/config.ts b/sites/main-site/src/content/config.ts index 1d14fedccf..2a3c40df02 100644 --- a/sites/main-site/src/content/config.ts +++ b/sites/main-site/src/content/config.ts @@ -119,6 +119,7 @@ const blog = defineCollection({ end: z.date().optional(), }) .optional(), + maxHeadingDepth: z.number().optional(), }) .refine((data) => { // Check if headerImage is present but headerImageAlt is not diff --git a/sites/main-site/src/pages/blog/[...blogpost].astro b/sites/main-site/src/pages/blog/[...blogpost].astro index feee180945..5b8d01b0aa 100644 --- a/sites/main-site/src/pages/blog/[...blogpost].astro +++ b/sites/main-site/src/pages/blog/[...blogpost].astro @@ -71,6 +71,7 @@ const md_github_url = 'https://github.com/nf-core/website/blob/main/sites/main-s viewTransitions={true} doubleNavbar={true} sidebarTitle="Blog posts" + maxHeadingDepth={Astro.props.post.data.maxHeadingDepth || 4} > { post.data.headerImage && post.data.embedHeaderImage !== undefined && post.data.embedHeaderImage !== false && ( From 5d8ed0b06e911745491118ae79096d271aa07dfe Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 14:51:13 +0200 Subject: [PATCH 27/35] remove duplicated text --- sites/main-site/src/content/blog/2024/tools-3_0_0.md | 11 ----------- 1 file changed, 11 deletions(-) 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.md index 92207b66c6..e783698b9b 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.md @@ -27,17 +27,6 @@ No worries, this is not as big of a change as the v2.0 release. The main things ## ✨ 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). -- [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) has replaced nf-validation in the pipeline template -- CI tests now use the nf-core tools version matching the pipeline's template version, reducing errors in PRs with each new tools release - -## ✨ 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. From a5ed7489e1d8eb0c17a2519922a3caf21a7e697f Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 16:35:28 +0200 Subject: [PATCH 28/35] add warning about python 3.8 EOL --- sites/main-site/src/content/blog/2024/tools-3_0_0.md | 1 + 1 file changed, 1 insertion(+) 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.md index e783698b9b..4cfda8abe7 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.md @@ -69,6 +69,7 @@ No worries, this is not as big of a change as the v2.0 release. The main things ## 🫡 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. # Tip: Avoiding Merge Conflicts From 1a3b2b86680ee9c3a224bf51277c8decf1ccba6e Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 16:47:17 +0200 Subject: [PATCH 29/35] update intro --- .../src/content/blog/2024/tools-3_0_0.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) 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.md index 4cfda8abe7..8e8b7bcf82 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.md @@ -13,17 +13,18 @@ label: maxHeadingDepth: 3 --- -# Previously on nf-core/tools +# What and Why? -We released nf-core/tools v2.0 in March 2021, which moved the template and tooling to DSL2 and introduced nf-core/modules commands. -In following releases we added subworkflows, switched to using nf-validation for schema validation and removed as much python code as possible from the template. -While this happened the nf-core community grew to now 10,000 slack members including 2,000 active users, who are working on 113 pipelines (compared to 49 when 2.0 was released), 1343 modules and 72 subworkflows. -With this growth we also saw new scientific areas being covered by nf-core pipelines, for example imaging data both on a [micro scale](https://nf-co.re/molkart/) and on a [global scale](https://nf-co.re/rangeland/). -This and the adoption of the nf-core template and tooling even outside the nf-core community, convinced us to make the nf-core template even more flexible and to improve the user experience of the nf-core/tools. +The nf-core/tools CLI is the backbone of our community. +It encapsulates the pipeline template that we use and packages and simplifies the tasks involved in keeping nf-core pipelines up to date. +The same holds true for modules and subworkflows. +In many ways, it is the linchpin of our collaborative coding. -# What's new in nf-core/tools v3.0.0 +This week, we are thrilled to announce nf-core/tools version 3.0.0. +With this release we bring much-requested template granularity, better findability for the many commands, and a suite of major updates to the nf-core pipeline template. +This blog post explains what's new and guides you through the update process. -No worries, this is not as big of a change as the v2.0 release. The main things are: +We promise, it's worth it! :pray: ## ✨ New features From 9320e470d152af9e63c8b9c7fd30b42867395297 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 16:55:48 +0200 Subject: [PATCH 30/35] add sub-bullets --- .../src/content/blog/2024/tools-3_0_0.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) 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.md index 8e8b7bcf82..804b963974 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.md @@ -29,15 +29,16 @@ 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. + - 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). -- [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) has replaced nf-validation in the pipeline template + - 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). +- [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) as a standard plugin in the template + - Replaces nf-validation for input validation - 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 + - This will reduce errors in opened PRs with each new tools release ## ⛓️‍💥 Breaking changes From f9cb3d96dfd5355ba69bed2aa50a7b788fe3fde7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 7 Oct 2024 16:58:50 +0200 Subject: [PATCH 31/35] Apply suggestions from code review Co-authored-by: Phil Ewels --- sites/main-site/src/content/blog/2024/tools-3_0_0.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) 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.md index 804b963974..ea827e48d0 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.md @@ -257,7 +257,7 @@ update: null See the [API docs](/docs/nf-core-tools/api_reference/dev/api/utils#pydantic-modelpythonnf_coreutilsnfcoretemplateconfigpython) for a more detailed description of each field and the allowed input values. -## `nextflow.conifg` +## `nextflow.config` Several merge conflicts due to changes described in [Important Template Updates](http://localhost:4321/blog/2024/tools-3_0_0#important-template-updates). @@ -265,9 +265,9 @@ Several merge conflicts due to changes described in [Important Template Updates] Double-check in the parameters section, that no pipeline-specific parameter would be removed by the incoming changes. In general, you can accept the incoming changes for this file. -## `subworkflows/local/utils_nfcore_$PIPELINE_NAME_pipeline/main.nf` +## Pipeline utils subworkflow -The switch to `nf-schema` might cause conflicts in the logic of reading in a samplesheet. +In `subworkflows/local/utils_nfcore_$PIPELINE_NAME_pipeline/main.nf` the switch to `nf-schema` might cause conflicts in the logic of reading in a samplesheet. #### Resolution From 5d72a36002f63e187624422bec2bb7b4590b7c29 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 17:03:25 +0200 Subject: [PATCH 32/35] change phrasing --- sites/main-site/src/content/blog/2024/tools-3_0_0.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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.md index 804b963974..397db91135 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.md @@ -35,8 +35,8 @@ We promise, it's worth it! :pray: - 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). -- [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) as a standard plugin in the template - - Replaces nf-validation for input validation +- 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 From 2700c5ff0d42bf53f75757756bccf8cd70ef77e4 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 8 Oct 2024 10:20:32 +0200 Subject: [PATCH 33/35] add asciinema recording of TUI --- sites/main-site/src/content/blog/2024/tools-3_0_0.md | 1 + 1 file changed, 1 insertion(+) 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.md index 6293c12f6c..76ebbd58d2 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.md @@ -35,6 +35,7 @@ We promise, it's worth it! :pray: - 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 From b988f583fd11fa2401c38ccf51879a9892638e75 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 8 Oct 2024 10:23:13 +0200 Subject: [PATCH 34/35] update embedded video --- sites/main-site/src/content/blog/2024/tools-3_0_0.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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.md index 76ebbd58d2..a14ef445e4 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.md @@ -35,7 +35,7 @@ We promise, it's worth it! :pray: - 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 From 29738a0885167b56d76660367b02bc506def39fe Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 8 Oct 2024 13:08:12 +0200 Subject: [PATCH 35/35] =?UTF-8?q?asciinema=20=F0=9F=91=8E=F0=9F=8F=BB=20yo?= =?UTF-8?q?tube=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 ```