Merge branch 'main' into fixes/gzip-check

.github/workflows/create-release.yml

@@ -25,6 +25,8 @@ jobs:
 
       - name: Build
         run: mvn install
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - uses: ncipollo/release-action@v1
         with:

.github/workflows/run-tests.yml

@@ -25,3 +25,5 @@ jobs:
 
       - name: Test
         run: mvn install
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -12,3 +12,4 @@ test_mock.nf
 site
 /tests
 /.nf-test.log
+/temp

README.md

@@ -8,13 +8,13 @@ The full documentation can be found [here](https://code.askimed.com/nf-test).
 nf-test has the same requirements as Nextflow and can be used on POSIX compatible systems like Linux or OS X. You can install nf-test using the following command:
 
 ```bash
-curl -fsSL https://code.askimed.com/install/nf-test | bash
+curl -fsSL https://get.nf-test.com | bash
 ```
 
 If you don't have curl installed, you could use wget:
 
 ```bash
-wget -qO- https://code.askimed.com/install/nf-test | bash
+wget -qO- https://get.nf-test.com | bash
 ```
 
 It will create the `nf-test` executable file in the current directory. Optionally, move the `nf-test` file to a directory accessible by your `$PATH` variable.
@@ -64,6 +64,12 @@ Show the world your Nextflow pipeline is using nf-test:
 [![nf-test](https://img.shields.io/badge/tested_with-nf--test-337ab7.svg)](https://github.com/askimed/nf-test)
 ```
 
+## Citation
+
+If you test your pipeline with nf-test, please cite:
+
+Forer, L., & Schönherr, S. (2024). Improving the Reliability and Quality of Nextflow Pipelines with nf-test. *bioRxiv*. [https://doi.org/10.1101/2024.05.25.595877](https://doi.org/10.1101/2024.05.25.595877)
+
 ## Contact
 
 - Lukas Forer [@lukfor](https://twitter.com/lukfor)

docs/docs/cli/coverage.md

@@ -0,0 +1,19 @@
+# `coverage` command
+
+:octicons-tag-24: 0.9.0
+
+## Usage
+
+```
+nf-test coverage
+```
+
+The `coverage` command prints information about the number of Nextflow files that are covered by a test.
+
+### Optional Arguments
+
+#### `--csv <filename>`
+Writes a coverage report in csv format.
+
+#### `--html <filename>`
+Writes a coverage report in html format.

docs/docs/cli/test.md

@@ -12,6 +12,10 @@ nf-test test [<NEXTFLOW_FILES>|<SCRIPT_FOLDERS>]
 
 To run your test using a specific Nextflow profile, you can use the `--profile` argument. [Learn more](/docs/docs/configuration#managing-profiles).
 
+#### `--dry-run`
+
+This flag allows users to simulate the execution of tests.
+
 #### `--verbose`
 
 Prints out the Nextflow output during test runs.
@@ -24,6 +28,12 @@ The Linux tool `procps` is required to run Nextflow tracing. In case your contai
 
 Execute only tests with the provided tag. Multiple tags can be used and have to be separated by commas (e.g. `tag1,tag2`).
 
+#### `--debug`
+
+The debug parameter prints out debugging messages and all available output channels which can be accessed in the `then` clause.
+
+### Output Reports
+
 #### `--tap <filename>`
 
 Writes test results in [TAP format](https://testanything.org) to file.
@@ -32,9 +42,66 @@ Writes test results in [TAP format](https://testanything.org) to file.
 
 Writes test results in [JUnit XML format](https://junit.org/) to file, which conforms to [the standard schema](https://github.com/junit-team/junit5/blob/242f3b3ef84cfd96c9de26992588812a68cdef8b/platform-tests/src/test/resources/jenkins-junit.xsd).
 
-#### `--debug`
+#### `--csv <filename>`
 
-The debug parameter prints out debugging messages and all available output channels which can be accessed in the `then` clause.
+Writes test results in csv file.
+
+#### `--ci`
+
+By default,nf-test automatically stores a new snapshot. When CI mode is activated, nf-test will fail the test instead of storing the snapshot automatically.
+
+
+### `--filter <types>`
+
+Filter test cases by specified types (e.g., module, pipeline, workflow or function). Multiple types can be separated by commas.
+
+
+### Optimizing Test Execution
+
+#### `--related-tests <files>`
+
+Finds and executes all related tests for the provided .nf or nf.test files. Multiple files can be provided space separated.
+
+#### `--follow-dependencies`
+
+When this flag is set, nf-test will traverse all dependencies when the related-tests flag is set.
+This option is particularly useful when you need to ensure that
+all dependent tests are executed, bypassing the firewall calculation process.
+
+#### `--only-changed`
+
+When enabled, this parameter instructs nf-test to execute tests only for files that have been modified within the
+current git working tree.
+
+#### `--changed-since <commit_hash|branch_name>`
+
+This parameter triggers the execution of tests related to changes made since the specifie commit.
+e.g. `--changed-since HEAD^` for all changes between the HEAD and HEAD - 1.
+
+#### `--changed-until <commit_hash|branch_name>`
+
+This parameter initiates the execution of tests related to changes made until the specified commit hash.
+
+#### `--graph <filename>`
+
+Enables the export of the dependency graph as a dot file.
+The dot file format is commonly used for representing graphs in graphviz and other related software.
+
+### Sharding 
+
+This parameter allows users to divide the execution workload into manageable chunks, which can be useful for
+parallel or distributed processing.
+
+#### `--shard <shard>`
+Splits the execution into arbitrary chunks defined by the format `i/n`, where `i` denotes the index of the current
+chunk and `n` represents the total number of chunks. For instance, `2/5` executes the second chunk out of five.
+
+#### `--shard-strategy <strategy>`
+Description: Specifies the strategy used to build shards when the `--shard` parameter is utilized.
+Accepted values are `round-robin` or `none.`. This parameter determines the method employed to distribute workload
+chunks among available resources. With the round-robin strategy, shards are distributed evenly among resources in
+a cyclic manner. The none strategy implies that shards won't be distributed automatically, and it's up to the
+user to manage the assignment of shards. Default value is `round-robin`.
 
 ## Examples
 
@@ -63,3 +130,29 @@ The debug parameter prints out debugging messages and all available output chann
   ```
   nf-test test --tap report.tap
   ```
+
+- Run all tests (and possible integration tests) for module `modules/module_a.nf` and `modules/module_b.nf`;
+
+  ```
+  nf-test test --related-tests modules/module_a.nf modules/module_b.nf
+  ```
+
+- If your project is a Git directory and you have modified files, you can run tests only for these changed files by
+using the following command:
+
+  ```
+  nf-test test --only-changed
+  ```
+
+- If you want to test all changes made between the current state of the repository and the last commit,
+you can use the following command:
+
+  ```
+  nf-test test --changed-since HEAD^
+  ```
+
+- Run only the second of four shards:
+
+  ```
+  nf-test test --shard 2/4 
+  ```

docs/docs/configuration.md

@@ -5,7 +5,7 @@
 The `nf-test.config` file is a configuration file used to customize settings and behavior for `nf-test`. This file must be located in the root of your project, and it is automatically loaded when you run `nf-test test`. Below are the parameters that can be adapted:
 
 | Parameter    | Description                                                                                                                                                        | Default Value             |
-| ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------- |
+|--------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------| ------------------------- |
 | `testsDir`   | Location for storing all nf-test cases (test scripts). If you want all test files to be in the same directory as the script itself, you can set the testDir to `.` | `"tests"`                 |
 | `workDir`    | Directory for storing temporary files and working directories for each test. This directory should be added to `.gitignore`.                                       | `".nf-test"`              |
 | `configFile` | Location of an optional `nextflow.config` file specifically used for executing tests. [Learn more](#testsnextflowconfig).                                          | `"tests/nextflow.config"` |
@@ -14,6 +14,9 @@ The `nf-test.config` file is a configuration file used to customize settings and
 | `withTrace`  | Enable or disable tracing options during testing. Disable tracing if your containers don't include the `procps` tool.                                              | `true`                    |
 | `autoSort`   | Enable or disable sorted channels by default when running tests.                                                                                                   | `true`                    |
 | `options`    | Custom Nextflow command-line options to be applied when running tests. For example `"-dump-channels -stub-run"`                                                    |                           |
+| `ignore`     | List of filenames or patterns that should be ignored when building the dependency graph. For example: `ignore 'folder/**/*.nf', 'modules/module.nf'`               | ``                        |
+| `triggers`   | List of filenames or patterns that should be trigger a full test run. For example: `triggers 'nextflow.config', 'test-data/**/*'`                                  | ``                        |
+| `requires`   | Can be used to specify the minimum required version of nf-test. Requires nf-test > 0.9.0                                                                           | ``                        |
 
 Here's an example of what an `nf-test.config` file could look like:
 
@@ -30,6 +33,17 @@ config {
 }
 ```
 
+The `requires` keyword can be used to specify the minimum required version of nf-test.
+For instance, to ensure the use of at least nf-test version 0.9.0, define it as follows:
+
+```groovy
+config {
+    requires (
+        "nf-test": "0.9.0"
+    )
+}
+```
+
 ## `tests/nextflow.config`
 
 This optional `nextflow.config` file is used to execute tests. This is a good place to set default `params` for all your tests. Example number of threads:
@@ -102,6 +116,10 @@ By understanding this profile evaluation order, you can effectively configure Ne
 
 ## File Staging
 
+!!! warning
+
+    File Staging is obsolete since version >= 0.9.0.
+
 The `stage` section of the `nf-test.config` file is used to define files that are needed by Nextflow in the test environment (`meta` directory). Additionally, the directories `lib`, `bin`, and `assets` are automatically staged.
 
 ### Supported Directives

docs/docs/plugins/using-plugins.md

@@ -13,7 +13,7 @@ For this purpose, we integrated the following plugin system that provides (a) th
 
 ## Using Plugins
 
-Available plugins are listed [here](https://code.askimed.com/nf-test-plugins).
+Available plugins are listed [here](https://plugins.nf-test.com).
 
 A plugin can be activated via the `nf-test.config` by adding the `plugin` section and by using `load` method to specify the plugin and its version:
 

docs/index.md

@@ -151,6 +151,15 @@ Show the world your Nextflow pipeline is using nf-test and add the following bad
 [![nf-test](https://img.shields.io/badge/tested_with-nf--test-337ab7.svg)](https://code.askimed.com/nf-test)
 ```
 
+---
+
+## :material-file: Citation
+
+If you test your pipeline with nf-test, please cite:
+
+Forer, L., & Schönherr, S. (2024). Improving the Reliability and Quality of Nextflow Pipelines with nf-test. *bioRxiv*. [https://doi.org/10.1101/2024.05.25.595877](https://doi.org/10.1101/2024.05.25.595877)
+
+
 ----
 
 ## :material-account-supervisor: About

docs/installation.md

@@ -5,13 +5,13 @@
 nf-test has the same requirements as Nextflow and can be used on POSIX compatible systems like Linux or OS X. You can install nf-test using the following command:
 
 ```bash
-curl -fsSL https://code.askimed.com/install/nf-test | bash
+curl -fsSL https://get.nf-test.com | bash
 ```
 
 If you don't have curl installed, you could use wget:
 
 ```bash
-wget -qO- https://code.askimed.com/install/nf-test | bash
+wget -qO- https://get.nf-test.com | bash
 ```
 
 It will create the `nf-test` executable file in the current directory. Optionally, move the `nf-test` file to a directory accessible by your `$PATH` variable.
@@ -48,7 +48,7 @@ Now you are ready to write your [first testcase](docs/getting-started.md).
 If you want to install a specific version pass it to the install script as so
 
 ```sh
-curl -fsSL https://code.askimed.com/install/nf-test | bash -s 0.7.0
+curl -fsSL https://get.nf-test.com | bash -s 0.7.0
 ```
 
 ### Manual installation

docs/resources.md

@@ -9,6 +9,22 @@ This page collects videos and blog posts about nf-test created by the community.
 
 ---
 
+### :material-tooltip-text:{ style="color: #337ab7" } Training Module: Hello nf-test
+
+This training modules introduces nf-test in a simple and easy to follow-along hello-nextflow style aimed for beginners.
+
+[hello nf-test training module](https://training.nextflow.io/hello_nextflow/05_hello_nf-test/)
+
+---
+
+### :material-tooltip-text:{ style="color: #337ab7" } Blog post: Leveraging nf-test for enhanced quality control in nf-core
+
+Reproducibility is an important attribute of all good science. This is specially true in the realm of bioinformatics, where software is hopefully being constantly updated, and pipelines are ideally being maintained. This blog post covers nf-test in the nf-core context.
+
+[Read blog post](https://nextflow.io/blog/2024/nf-test-in-nf-core.html)
+
+---
+
 ### :fontawesome-brands-youtube:{ style="color: #EE0F0F" } nf-core/bytesize: Converting pytest modules to nf-test
 
 **Adam Talbot** & **Sateesh Peri** do a live demo of converting nf-core DSL2 modules pytests to nf-test

docs/tutorials.md

@@ -0,0 +1,16 @@
+---
+hide:
+  - navigation
+---
+
+# Tutorials
+
+---
+
+### [:material-file:{ style="color: #337ab7" } Setup nf-test on GitHub Actions](tutorials/github-actions.md)
+
+In this tutorial, we will guide you through setting up and running `nf-test` on GitHub Actions.
+
+[Read tutorial](tutorials/github-actions.md)
+
+---