nf-core 2.9__tar.gz → 2.11__tar.gz

{nf-core-2.9/nf_core.egg-info → nf-core-2.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nf-core
-Version: 2.9
+Version: 2.11
 Summary: Helper tools for use with nf-core Nextflow pipelines.
 Home-page: https://github.com/nf-core/tools
 Author: Phil Ewels
@@ -10,6 +10,26 @@ Keywords: nf-core,nextflow,bioinformatics,workflow,pipeline,biology,sequencing,N
 Requires-Python: >=3.8, <4
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: click
+Requires-Dist: filetype
+Requires-Dist: GitPython
+Requires-Dist: jinja2
+Requires-Dist: jsonschema>=3.0
+Requires-Dist: markdown>=3.3
+Requires-Dist: packaging
+Requires-Dist: pre-commit
+Requires-Dist: prompt_toolkit>=3.0.3
+Requires-Dist: pytest>=7.0.0
+Requires-Dist: pytest-workflow>=1.6.0
+Requires-Dist: pyyaml
+Requires-Dist: questionary>=1.8.0
+Requires-Dist: refgenie
+Requires-Dist: requests
+Requires-Dist: requests_cache
+Requires-Dist: rich-click>=1.6.1
+Requires-Dist: rich>=13.3.1
+Requires-Dist: tabulate
+Requires-Dist: pdiff
 
 # ![nf-core/tools](docs/images/nfcore-tools_logo_light.png#gh-light-mode-only) ![nf-core/tools](docs/images/nfcore-tools_logo_dark.png#gh-dark-mode-only) <!-- omit in toc -->
 
@@ -33,6 +53,7 @@ A python package with helper tools for the nf-core community.
 - [`nf-core` tools update](#update-tools)
 - [`nf-core list` - List available pipelines](#listing-pipelines)
 - [`nf-core launch` - Run a pipeline with interactive parameter prompts](#launch-a-pipeline)
+- [`nf-core create-params-file` - Create a parameter file](#create-a-parameter-file)
 - [`nf-core download` - Download a pipeline for offline use](#downloading-pipelines-for-offline-use)
 - [`nf-core licences` - List software licences in a pipeline](#pipeline-software-licences)
 - [`nf-core create` - Create a new pipeline with the nf-core template](#creating-a-new-pipeline)
@@ -51,7 +72,6 @@ A python package with helper tools for the nf-core community.
   - [`modules remove` - Remove a module from a pipeline](#remove-a-module-from-a-pipeline)
   - [`modules patch` - Create a patch file for a module](#create-a-patch-file-for-a-module)
   - [`modules create` - Create a module from the template](#create-a-new-module)
-  - [`modules create-test-yml` - Create the `test.yml` file for a module](#create-a-module-test-config-file)
   - [`modules lint` - Check a module against nf-core guidelines](#check-a-module-against-nf-core-guidelines)
   - [`modules test` - Run the tests for a module](#run-the-tests-for-a-module-using-pytest)
   - [`modules bump-versions` - Bump software versions of modules](#bump-bioconda-and-container-versions-of-modules-in)
@@ -65,12 +85,12 @@ A python package with helper tools for the nf-core community.
   - [`subworkflows update` - Update subworkflows in a pipeline](#update-subworkflows-in-a-pipeline)
   - [`subworkflows remove` - Remove a subworkflow from a pipeline](#remove-a-subworkflow-from-a-pipeline)
   - [`subworkflows create` - Create a subworkflow from the template](#create-a-new-subworkflow)
-  - [`subworkflows create-test-yml` - Create the `test.yml` file for a subworkflow](#create-a-subworkflow-test-config-file)
+  - [`subworkflows lint` - Check a subworkflow against nf-core guidelines](#check-a-subworkflow-against-nf-core-guidelines)
   - [`subworkflows test` - Run the tests for a subworkflow](#run-the-tests-for-a-subworkflow-using-pytest)
 - [Citation](#citation)
 
 The nf-core tools package is written in Python and can be imported and used within other packages.
-For documentation of the internal Python functions, please refer to the [Tools Python API docs](https://nf-co.re/tools-docs/).
+For documentation of the internal Python functions, please refer to the [Tools Python API docs](https://nf-co.re/tools/docs/).
 
 ## Installation
 
@@ -89,7 +109,7 @@ conda install nf-core
 Alternatively, you can create a new environment with both nf-core/tools and nextflow:
 
 ```bash
-conda create --name nf-core python=3.8 nf-core nextflow
+conda create --name nf-core python=3.11 nf-core nextflow
 conda activate nf-core
 ```
 
@@ -199,7 +219,7 @@ for wf in wfs.remote_workflows:
     print(wf.full_name)
 ```
 
-Please see [https://nf-co.re/tools-docs/](https://nf-co.re/tools-docs/) for the function documentation.
+Please see [https://nf-co.re/tools/docs/](https://nf-co.re/tools/docs/) for the function documentation.
 
 ### Automatic version check
 
@@ -238,10 +258,12 @@ Auto-completion for the `nf-core` command is available for bash, zsh and fish. T
 
 After a restart of the shell session you should have auto-completion for the `nf-core` command and all its sub-commands and options.
 
-> **NB:** The added line will run the command `nf-core` (which will also slow down startup time of your shell). You should therefore either have the nf-core/tools installed globally.
+> [!NOTE]
+> The added line will run the command `nf-core` (which will also slow down startup time of your shell). You should therefore either have the nf-core/tools installed globally.
 > You can also wrap it inside `if type nf-core > /dev/null; then ` \<YOUR EVAL CODE LINE\> `fi` for bash and zsh or `if command -v nf-core &> /dev/null eval (env _NF_CORE_COMPLETE=fish_source nf-core) end` for fish. You need to then source the config in your environment for the completions to be activated.
 
-> **NB:** If you see the error `command not found compdef` , be sure that your config file contains the line `autoload -Uz compinit && compinit` before the eval line.
+> [!TIP]
+> If you see the error `command not found compdef` , be sure that your config file contains the line `autoload -Uz compinit && compinit` before the eval line.
 
 ## Listing pipelines
 
@@ -324,6 +346,22 @@ Do you want to run this command now?  [y/n]:
 - `--url`
   - Change the URL used for the graphical interface, useful for development work on the website.
 
+## Create a parameter file
+
+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.
+
+You can create a parameter file with all parameters of a pipeline with the `nf-core 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,
+or the path to a directory containing a Nextflow pipeline _(can be any pipeline, doesn't have to be nf-core)_.
+
+The generated YAML file contains all parameters set to the pipeline default value along with their description in comments.
+This template can then be used by uncommenting and modifying the value of parameters you want to pass to a pipline run.
+
+Hidden options are not included by default, but can be included using the `-x`/`--show-hidden` flag.
+
 ## Downloading pipelines for offline use
 
 Sometimes you may need to run an nf-core pipeline on a server or HPC system that has no internet connection.
@@ -356,14 +394,16 @@ You can run the pipeline by simply providing the directory path for the `workflo
 nextflow run /path/to/download/nf-core-rnaseq-dev/workflow/ --input mydata.csv --outdir results  # usual parameters here
 ```
 
-> Note that if you downloaded Singularity container images, you will need to use `-profile singularity` or have it enabled in your config file.
+> [!NOTE]
+> If you downloaded Singularity container images, you will need to use `-profile singularity` or have it enabled in your config file.
 
 ### Downloaded nf-core configs
 
 The pipeline files are automatically updated (`params.custom_config_base` is set to `../configs`), so that the local copy of institutional configs are available when running the pipeline.
 So using `-profile <NAME>` should work if available within [nf-core/configs](https://github.com/nf-core/configs).
 
-> ⚠️ This option is not available when downloading a pipeline for use with [Nextflow Tower](#adapting-downloads-to-nextflow-tower) because the application manages all configurations separately.
+> [!WARNING]
+> This option is not available when downloading a pipeline for use with [Nextflow Tower](#adapting-downloads-to-nextflow-tower) because the application manages all configurations separately.
 
 ### Downloading Apptainer containers
 
@@ -421,14 +461,16 @@ If the download speeds are much slower than your internet connection is capable
 
 Subsequently, the `*.git` folder can be moved to it's final destination and linked with a pipeline in _Tower_ using the `file:/` prefix.
 
-> 💡 Also without access to Tower, pipelines downloaded with the `--tower` flag can be run: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
+> [!TIP]
+> Also without access to Tower, pipelines downloaded with the `--tower` flag can be run if the _absolute_ path is specified: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
 
 ## Pipeline software licences
 
 Sometimes it's useful to see the software licences of the tools used in a pipeline.
 You can use the `licences` subcommand to fetch and print the software licence from each conda / PyPI package used in an nf-core pipeline.
 
-> ⚠️ This command does not currently work for newer DSL2 pipelines. This will hopefully be addressed [soon](https://github.com/nf-core/tools/issues/1155).
+> [!WARNING]
+> This command does not currently work for newer DSL2 pipelines. This will hopefully be addressed [soon](https://github.com/nf-core/tools/issues/1155).
 
 <!-- RICH-CODEX
 timeout: 10
@@ -456,6 +498,7 @@ You can then continue to edit, commit and push normally as you build your pipeli
 
 Please see the [nf-core documentation](https://nf-co.re/developers/adding_pipelines) 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!
 > See the [documentation](https://nf-co.re/developers/adding_pipelines#join-the-community) for instructions.
 
@@ -516,7 +559,7 @@ Each test result name on the left is a terminal hyperlink.
 In most terminals you can <kbd>ctrl</kbd> + <kbd>click</kbd> ( <kbd>cmd</kbd> + <kbd>click</kbd>) these
 links to open documentation specific to this test in your browser.
 
-Alternatively visit <https://nf-co.re/tools-docs/lint_tests/index.html> and find your test to read more.
+Alternatively visit <https://nf-co.re/tools/docs/latest/pipeline_lint_tests/index.html> and find your test to read more.
 
 ### Linting config
 
@@ -928,20 +971,6 @@ fake_command: nf-core modules create fastqc --author @nf-core-bot  --label proce
 
 ![`cd modules && nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force`](docs/images/nf-core-modules-create.svg)
 
-### Create a module test config file
-
-All modules on [nf-core/modules](https://github.com/nf-core/modules) have a strict requirement of being unit tested using minimal test data.
-To help developers build new modules, the `nf-core modules create-test-yml` command automates the creation of the yaml file required to document the output file `md5sum` and other information generated by the testing.
-After you have written a minimal Nextflow script to test your module `tests/modules/<tool>/<subtool>/main.nf`, this command will run the tests for you and create the `tests/modules/<tool>/<subtool>/test.yml` file.
-
-<!-- RICH-CODEX
-working_dir: tmp/modules
-extra_env:
-  PROFILE: 'conda'
--->
-
-![`nf-core modules create-test-yml fastqc --no-prompts --force`](docs/images/nf-core-modules-create-test.svg)
-
 ### Check a module against nf-core guidelines
 
 Run the `nf-core modules lint` command to check modules in the current working directory (pipeline or nf-core/modules clone) against nf-core guidelines.
@@ -955,13 +984,12 @@ before_command: sed 's/1.13a/1.10/g' modules/multiqc/main.nf > modules/multiqc/m
 
 ![`nf-core modules lint multiqc`](docs/images/nf-core-modules-lint.svg)
 
-### Run the tests for a module using pytest
+### Create a test for a module
 
-To run unit tests of a module that you have installed or the test created by the command [`nf-core modules create-test-yml`](#create-a-module-test-config-file), you can use `nf-core modules test` command. This command runs the tests specified in `modules/tests/software/<tool>/<subtool>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).
+All modules on [nf-core/modules](https://github.com/nf-core/modules) have a strict requirement of being unit tested using minimal test data. We use [nf-test](https://code.askimed.com/nf-test/) as our testing framework.
+Each module comes already with a template for the test file in `test/main.nf.test`. Replace the placeholder code in that file with your specific input, output and proces. In order to generate the corresponding snapshot after writing your test, you can use the `nf-core modules test` command. This command will run `nf-test test` twice, to also check for snapshot stability, i.e. that the same snapshot is generated on multiple runs.
 
-> This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new module to add the new files to your git index.
-
-You can specify the module name in the form TOOL/SUBTOOL in command line or provide it later by prompts.
+You can specify the module name in the form TOOL/SUBTOOL in the command or provide it later through interactive prompts.
 
 <!-- RICH-CODEX
 working_dir: tmp/modules
@@ -970,7 +998,15 @@ extra_env:
   PROFILE: 'conda'
 -->
 
-![`nf-core modules test samtools/view --no-prompts`](docs/images/nf-core-modules-test.svg)
+![`nf-core modules test fastqc --no-prompts --force`](docs/images/nf-core-modules-test.svg)
+
+In case you changed something in the test and want to update the snapshot, run
+
+```bash
+nf-core modules test --update
+```
+
+If you want to run the test only once without checking for snapshot stability, you can use the `--once` flag.
 
 ### Bump bioconda and container versions of modules in
 
@@ -1200,36 +1236,43 @@ fake_command: nf-core subworkflows create bam_stats_samtools --author @nf-core-b
 
 ![`nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force`](docs/images/nf-core-subworkflows-create.svg)
 
-### Create a subworkflow test config file
+### Create a test for a subworkflow
 
-All subworkflows on [nf-core/modules](https://github.com/nf-core/modules) have a strict requirement of being unit tested using minimal test data.
-To help developers build new subworkflows, the `nf-core subworkflows create-test-yml` command automates the creation of the yaml file required to document the output file `md5sum` and other information generated by the testing.
-After you have written a minimal Nextflow script to test your subworkflow in `/tests/subworkflow/<subworkflow_name>/main.nf`, this command will run the tests for you and create the `/tests/subworkflow/<tool>/<subtool>/test.yml` file.
+All subworkflows on [nf-core/modules](https://github.com/nf-core/modules) have a strict requirement of being unit tested using minimal test data. We use [nf-test](https://code.askimed.com/nf-test/) as our testing framework.
+Each subworkflow comes already with a template for the test file in `test/main.nf.test`. Replace the placeholder code in that file with your specific input, output and proces. In order to generate the corresponding snapshot after writing your test, you can use the `nf-core subworkflows test` command. This command will run `nf-test test` twice, to also check for snapshot stability, i.e. that the same snapshot is generated on multiple runs.
+
+You can specify the subworkflow name in the command or provide it later through interactive prompts.
 
 <!-- RICH-CODEX
 working_dir: tmp/modules
+timeout: 30
 extra_env:
   PROFILE: 'conda'
 -->
 
-![`nf-core subworkflows create-test-yml bam_stats_samtools --no-prompts --force`](docs/images/nf-core-subworkflows-create-test.svg)
+![`nf-core subworkflows test bam_rseqc --no-prompts`](docs/images/nf-core-subworkflows-test.svg)
+
+In case you changed something in the test and want to update the snapshot, run
 
-### Run the tests for a subworkflow using pytest
+```bash
+nf-core subworkflows test --update
+```
 
-To run unit tests of a subworkflow that you have installed or the test created by the command [`nf-core subworkflow create-test-yml`](#create-a-subworkflow-test-config-file), you can use `nf-core subworkflows test` command. This command runs the tests specified in `tests/subworkflows/<subworkflow_name>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).
+If you want to run the test only once without checking for snapshot stability, you can use the `--once` flag.
 
-> This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new subworkflow to add the new files to your git index.
+### Check a subworkflow against nf-core guidelines
 
-You can specify the subworkflow name in the form TOOL/SUBTOOL in command line or provide it later by prompts.
+Run the `nf-core subworkflows lint` command to check subworkflows in the current working directory (a pipeline or a clone of nf-core/modules) against nf-core guidelines.
+
+Use the `--all` flag to run linting on all subworkflows found. Use `--dir <pipeline_dir>` to specify a different directory than the current working directory.
 
 <!-- RICH-CODEX
 working_dir: tmp/modules
-timeout: 30
 extra_env:
   PROFILE: 'conda'
 -->
 
-![`nf-core subworkflows test bam_rseqc --no-prompts`](docs/images/nf-core-subworkflows-test.svg)
+![`nf-core subworkflows lint bam_stats_samtools`](docs/images/nf-core-subworkflows-lint.svg)
 
 ## Citation
 

{nf-core-2.9 → nf-core-2.11}/README.md

@@ -20,6 +20,7 @@ A python package with helper tools for the nf-core community.
 - [`nf-core` tools update](#update-tools)
 - [`nf-core list` - List available pipelines](#listing-pipelines)
 - [`nf-core launch` - Run a pipeline with interactive parameter prompts](#launch-a-pipeline)
+- [`nf-core create-params-file` - Create a parameter file](#create-a-parameter-file)
 - [`nf-core download` - Download a pipeline for offline use](#downloading-pipelines-for-offline-use)
 - [`nf-core licences` - List software licences in a pipeline](#pipeline-software-licences)
 - [`nf-core create` - Create a new pipeline with the nf-core template](#creating-a-new-pipeline)
@@ -38,7 +39,6 @@ A python package with helper tools for the nf-core community.
   - [`modules remove` - Remove a module from a pipeline](#remove-a-module-from-a-pipeline)
   - [`modules patch` - Create a patch file for a module](#create-a-patch-file-for-a-module)
   - [`modules create` - Create a module from the template](#create-a-new-module)
-  - [`modules create-test-yml` - Create the `test.yml` file for a module](#create-a-module-test-config-file)
   - [`modules lint` - Check a module against nf-core guidelines](#check-a-module-against-nf-core-guidelines)
   - [`modules test` - Run the tests for a module](#run-the-tests-for-a-module-using-pytest)
   - [`modules bump-versions` - Bump software versions of modules](#bump-bioconda-and-container-versions-of-modules-in)
@@ -52,12 +52,12 @@ A python package with helper tools for the nf-core community.
   - [`subworkflows update` - Update subworkflows in a pipeline](#update-subworkflows-in-a-pipeline)
   - [`subworkflows remove` - Remove a subworkflow from a pipeline](#remove-a-subworkflow-from-a-pipeline)
   - [`subworkflows create` - Create a subworkflow from the template](#create-a-new-subworkflow)
-  - [`subworkflows create-test-yml` - Create the `test.yml` file for a subworkflow](#create-a-subworkflow-test-config-file)
+  - [`subworkflows lint` - Check a subworkflow against nf-core guidelines](#check-a-subworkflow-against-nf-core-guidelines)
   - [`subworkflows test` - Run the tests for a subworkflow](#run-the-tests-for-a-subworkflow-using-pytest)
 - [Citation](#citation)
 
 The nf-core tools package is written in Python and can be imported and used within other packages.
-For documentation of the internal Python functions, please refer to the [Tools Python API docs](https://nf-co.re/tools-docs/).
+For documentation of the internal Python functions, please refer to the [Tools Python API docs](https://nf-co.re/tools/docs/).
 
 ## Installation
 
@@ -76,7 +76,7 @@ conda install nf-core
 Alternatively, you can create a new environment with both nf-core/tools and nextflow:
 
 ```bash
-conda create --name nf-core python=3.8 nf-core nextflow
+conda create --name nf-core python=3.11 nf-core nextflow
 conda activate nf-core
 ```
 
@@ -186,7 +186,7 @@ for wf in wfs.remote_workflows:
     print(wf.full_name)
 ```
 
-Please see [https://nf-co.re/tools-docs/](https://nf-co.re/tools-docs/) for the function documentation.
+Please see [https://nf-co.re/tools/docs/](https://nf-co.re/tools/docs/) for the function documentation.
 
 ### Automatic version check
 
@@ -225,10 +225,12 @@ Auto-completion for the `nf-core` command is available for bash, zsh and fish. T
 
 After a restart of the shell session you should have auto-completion for the `nf-core` command and all its sub-commands and options.
 
-> **NB:** The added line will run the command `nf-core` (which will also slow down startup time of your shell). You should therefore either have the nf-core/tools installed globally.
+> [!NOTE]
+> The added line will run the command `nf-core` (which will also slow down startup time of your shell). You should therefore either have the nf-core/tools installed globally.
 > You can also wrap it inside `if type nf-core > /dev/null; then ` \<YOUR EVAL CODE LINE\> `fi` for bash and zsh or `if command -v nf-core &> /dev/null eval (env _NF_CORE_COMPLETE=fish_source nf-core) end` for fish. You need to then source the config in your environment for the completions to be activated.
 
-> **NB:** If you see the error `command not found compdef` , be sure that your config file contains the line `autoload -Uz compinit && compinit` before the eval line.
+> [!TIP]
+> If you see the error `command not found compdef` , be sure that your config file contains the line `autoload -Uz compinit && compinit` before the eval line.
 
 ## Listing pipelines
 
@@ -311,6 +313,22 @@ Do you want to run this command now?  [y/n]:
 - `--url`
   - Change the URL used for the graphical interface, useful for development work on the website.
 
+## Create a parameter file
+
+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.
+
+You can create a parameter file with all parameters of a pipeline with the `nf-core 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,
+or the path to a directory containing a Nextflow pipeline _(can be any pipeline, doesn't have to be nf-core)_.
+
+The generated YAML file contains all parameters set to the pipeline default value along with their description in comments.
+This template can then be used by uncommenting and modifying the value of parameters you want to pass to a pipline run.
+
+Hidden options are not included by default, but can be included using the `-x`/`--show-hidden` flag.
+
 ## Downloading pipelines for offline use
 
 Sometimes you may need to run an nf-core pipeline on a server or HPC system that has no internet connection.
@@ -343,14 +361,16 @@ You can run the pipeline by simply providing the directory path for the `workflo
 nextflow run /path/to/download/nf-core-rnaseq-dev/workflow/ --input mydata.csv --outdir results  # usual parameters here
 ```
 
-> Note that if you downloaded Singularity container images, you will need to use `-profile singularity` or have it enabled in your config file.
+> [!NOTE]
+> If you downloaded Singularity container images, you will need to use `-profile singularity` or have it enabled in your config file.
 
 ### Downloaded nf-core configs
 
 The pipeline files are automatically updated (`params.custom_config_base` is set to `../configs`), so that the local copy of institutional configs are available when running the pipeline.
 So using `-profile <NAME>` should work if available within [nf-core/configs](https://github.com/nf-core/configs).
 
-> ⚠️ This option is not available when downloading a pipeline for use with [Nextflow Tower](#adapting-downloads-to-nextflow-tower) because the application manages all configurations separately.
+> [!WARNING]
+> This option is not available when downloading a pipeline for use with [Nextflow Tower](#adapting-downloads-to-nextflow-tower) because the application manages all configurations separately.
 
 ### Downloading Apptainer containers
 
@@ -408,14 +428,16 @@ If the download speeds are much slower than your internet connection is capable
 
 Subsequently, the `*.git` folder can be moved to it's final destination and linked with a pipeline in _Tower_ using the `file:/` prefix.
 
-> 💡 Also without access to Tower, pipelines downloaded with the `--tower` flag can be run: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
+> [!TIP]
+> Also without access to Tower, pipelines downloaded with the `--tower` flag can be run if the _absolute_ path is specified: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
 
 ## Pipeline software licences
 
 Sometimes it's useful to see the software licences of the tools used in a pipeline.
 You can use the `licences` subcommand to fetch and print the software licence from each conda / PyPI package used in an nf-core pipeline.
 
-> ⚠️ This command does not currently work for newer DSL2 pipelines. This will hopefully be addressed [soon](https://github.com/nf-core/tools/issues/1155).
+> [!WARNING]
+> This command does not currently work for newer DSL2 pipelines. This will hopefully be addressed [soon](https://github.com/nf-core/tools/issues/1155).
 
 <!-- RICH-CODEX
 timeout: 10
@@ -443,6 +465,7 @@ You can then continue to edit, commit and push normally as you build your pipeli
 
 Please see the [nf-core documentation](https://nf-co.re/developers/adding_pipelines) 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!
 > See the [documentation](https://nf-co.re/developers/adding_pipelines#join-the-community) for instructions.
 
@@ -503,7 +526,7 @@ Each test result name on the left is a terminal hyperlink.
 In most terminals you can <kbd>ctrl</kbd> + <kbd>click</kbd> ( <kbd>cmd</kbd> + <kbd>click</kbd>) these
 links to open documentation specific to this test in your browser.
 
-Alternatively visit <https://nf-co.re/tools-docs/lint_tests/index.html> and find your test to read more.
+Alternatively visit <https://nf-co.re/tools/docs/latest/pipeline_lint_tests/index.html> and find your test to read more.
 
 ### Linting config
 
@@ -915,20 +938,6 @@ fake_command: nf-core modules create fastqc --author @nf-core-bot  --label proce
 
 ![`cd modules && nf-core modules create fastqc --author @nf-core-bot  --label process_low --meta --force`](docs/images/nf-core-modules-create.svg)
 
-### Create a module test config file
-
-All modules on [nf-core/modules](https://github.com/nf-core/modules) have a strict requirement of being unit tested using minimal test data.
-To help developers build new modules, the `nf-core modules create-test-yml` command automates the creation of the yaml file required to document the output file `md5sum` and other information generated by the testing.
-After you have written a minimal Nextflow script to test your module `tests/modules/<tool>/<subtool>/main.nf`, this command will run the tests for you and create the `tests/modules/<tool>/<subtool>/test.yml` file.
-
-<!-- RICH-CODEX
-working_dir: tmp/modules
-extra_env:
-  PROFILE: 'conda'
--->
-
-![`nf-core modules create-test-yml fastqc --no-prompts --force`](docs/images/nf-core-modules-create-test.svg)
-
 ### Check a module against nf-core guidelines
 
 Run the `nf-core modules lint` command to check modules in the current working directory (pipeline or nf-core/modules clone) against nf-core guidelines.
@@ -942,13 +951,12 @@ before_command: sed 's/1.13a/1.10/g' modules/multiqc/main.nf > modules/multiqc/m
 
 ![`nf-core modules lint multiqc`](docs/images/nf-core-modules-lint.svg)
 
-### Run the tests for a module using pytest
+### Create a test for a module
 
-To run unit tests of a module that you have installed or the test created by the command [`nf-core modules create-test-yml`](#create-a-module-test-config-file), you can use `nf-core modules test` command. This command runs the tests specified in `modules/tests/software/<tool>/<subtool>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).
+All modules on [nf-core/modules](https://github.com/nf-core/modules) have a strict requirement of being unit tested using minimal test data. We use [nf-test](https://code.askimed.com/nf-test/) as our testing framework.
+Each module comes already with a template for the test file in `test/main.nf.test`. Replace the placeholder code in that file with your specific input, output and proces. In order to generate the corresponding snapshot after writing your test, you can use the `nf-core modules test` command. This command will run `nf-test test` twice, to also check for snapshot stability, i.e. that the same snapshot is generated on multiple runs.
 
-> This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new module to add the new files to your git index.
-
-You can specify the module name in the form TOOL/SUBTOOL in command line or provide it later by prompts.
+You can specify the module name in the form TOOL/SUBTOOL in the command or provide it later through interactive prompts.
 
 <!-- RICH-CODEX
 working_dir: tmp/modules
@@ -957,7 +965,15 @@ extra_env:
   PROFILE: 'conda'
 -->
 
-![`nf-core modules test samtools/view --no-prompts`](docs/images/nf-core-modules-test.svg)
+![`nf-core modules test fastqc --no-prompts --force`](docs/images/nf-core-modules-test.svg)
+
+In case you changed something in the test and want to update the snapshot, run
+
+```bash
+nf-core modules test --update
+```
+
+If you want to run the test only once without checking for snapshot stability, you can use the `--once` flag.
 
 ### Bump bioconda and container versions of modules in
 
@@ -1187,36 +1203,43 @@ fake_command: nf-core subworkflows create bam_stats_samtools --author @nf-core-b
 
 ![`nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force`](docs/images/nf-core-subworkflows-create.svg)
 
-### Create a subworkflow test config file
+### Create a test for a subworkflow
 
-All subworkflows on [nf-core/modules](https://github.com/nf-core/modules) have a strict requirement of being unit tested using minimal test data.
-To help developers build new subworkflows, the `nf-core subworkflows create-test-yml` command automates the creation of the yaml file required to document the output file `md5sum` and other information generated by the testing.
-After you have written a minimal Nextflow script to test your subworkflow in `/tests/subworkflow/<subworkflow_name>/main.nf`, this command will run the tests for you and create the `/tests/subworkflow/<tool>/<subtool>/test.yml` file.
+All subworkflows on [nf-core/modules](https://github.com/nf-core/modules) have a strict requirement of being unit tested using minimal test data. We use [nf-test](https://code.askimed.com/nf-test/) as our testing framework.
+Each subworkflow comes already with a template for the test file in `test/main.nf.test`. Replace the placeholder code in that file with your specific input, output and proces. In order to generate the corresponding snapshot after writing your test, you can use the `nf-core subworkflows test` command. This command will run `nf-test test` twice, to also check for snapshot stability, i.e. that the same snapshot is generated on multiple runs.
+
+You can specify the subworkflow name in the command or provide it later through interactive prompts.
 
 <!-- RICH-CODEX
 working_dir: tmp/modules
+timeout: 30
 extra_env:
   PROFILE: 'conda'
 -->
 
-![`nf-core subworkflows create-test-yml bam_stats_samtools --no-prompts --force`](docs/images/nf-core-subworkflows-create-test.svg)
+![`nf-core subworkflows test bam_rseqc --no-prompts`](docs/images/nf-core-subworkflows-test.svg)
+
+In case you changed something in the test and want to update the snapshot, run
 
-### Run the tests for a subworkflow using pytest
+```bash
+nf-core subworkflows test --update
+```
 
-To run unit tests of a subworkflow that you have installed or the test created by the command [`nf-core subworkflow create-test-yml`](#create-a-subworkflow-test-config-file), you can use `nf-core subworkflows test` command. This command runs the tests specified in `tests/subworkflows/<subworkflow_name>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).
+If you want to run the test only once without checking for snapshot stability, you can use the `--once` flag.
 
-> This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new subworkflow to add the new files to your git index.
+### Check a subworkflow against nf-core guidelines
 
-You can specify the subworkflow name in the form TOOL/SUBTOOL in command line or provide it later by prompts.
+Run the `nf-core subworkflows lint` command to check subworkflows in the current working directory (a pipeline or a clone of nf-core/modules) against nf-core guidelines.
+
+Use the `--all` flag to run linting on all subworkflows found. Use `--dir <pipeline_dir>` to specify a different directory than the current working directory.
 
 <!-- RICH-CODEX
 working_dir: tmp/modules
-timeout: 30
 extra_env:
   PROFILE: 'conda'
 -->
 
-![`nf-core subworkflows test bam_rseqc --no-prompts`](docs/images/nf-core-subworkflows-test.svg)
+![`nf-core subworkflows lint bam_stats_samtools`](docs/images/nf-core-subworkflows-lint.svg)
 
 ## Citation