First commit

.github/workflows/build.yml

@@ -0,0 +1,45 @@
+name: nf-hello CI
+on:
+  push:
+    branches:
+      - '*'
+    tags-ignore:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+jobs:
+  build:
+    name: Build nf-hello
+    if: "!contains(github.event.head_commit.message, '[ci skip]')"
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    strategy:
+      fail-fast: false
+      matrix:
+        java_version: [8, 11]
+
+    steps:
+      - name: Environment
+        run: env | sort
+
+      - name: Checkout
+        uses: actions/checkout@v1
+        with:
+          fetch-depth: 1
+          submodules: true
+
+      - name: Setup Java ${{ matrix.java_version }}
+        uses: actions/setup-java@v1
+        with:
+          java-version: ${{matrix.java_version}}
+          architecture: x64
+
+      - name: Compile
+        run: ./gradlew assemble
+
+      - name: Tests
+        run: ./gradlew check
+        env:
+          GRADLE_OPTS: '-Dorg.gradle.daemon=false'
+

.gitignore

@@ -0,0 +1,9 @@
+# Ignore Gradle project-specific cache directory
+.gradle
+.idea
+.nextflow
+
+# Ignore Gradle build output directory
+build
+work
+out

COPYING

@@ -0,0 +1,176 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+

Makefile

@@ -0,0 +1,60 @@
+
+config ?= compileClasspath
+
+ifdef module 
+mm = :${module}:
+else 
+mm = 
+endif 
+
+clean:
+	./gradlew clean
+
+compile:
+	./gradlew compileGroovy
+	@echo "DONE `date`"
+
+
+check:
+	./gradlew check
+
+
+#
+# Show dependencies try `make deps config=runtime`, `make deps config=google`
+#
+deps:
+	./gradlew -q ${mm}dependencies --configuration ${config}
+
+deps-all:
+	./gradlew -q dependencyInsight --configuration ${config} --dependency ${module}
+
+#
+# Refresh SNAPSHOTs dependencies
+#
+refresh:
+	./gradlew --refresh-dependencies 
+
+#
+# Run all tests or selected ones
+#
+test:
+ifndef class
+	./gradlew ${mm}test
+else
+	./gradlew ${mm}test --tests ${class}
+endif
+
+
+
+#
+# Upload JAR artifacts to Maven Central
+#
+upload:
+	./gradlew upload
+
+
+upload-plugins:
+	./gradlew plugins:upload
+
+publish-index:
+	./gradlew plugins:publishIndex

README.md

@@ -0,0 +1,103 @@
+# nf-hello plugin 
+
+This project shows how to implement a simple Nextflow plugin named `nf-hello` that intercepts 
+workflow execution events to print a message when the execution starts and on workflow completion.
+
+## Plugin assets 
+                    
+- `settings.gradle`
+
+    Gradle project settings. 
+
+- `plugins/nf-hello`
+
+    The plugin implementation base directory.
+
+- `plugins/nf-hello/build.gradle` 
+
+    Plugin Gradle build file. Project dependencies should be added here.
+
+- `plugins/nf-hello/src/resources/META-INF/MANIFEST.MF` 
+
+    Manifest file defining the plugin attributes e.g. name, version, etc.
+    The attribute `Plugin-Class` declares the plugin main class. This class 
+    should extend the base class `nextflow.plugin.BasePlugin` e.g. 
+    `nextflow.hello.HelloPlugin`.
+
+- `plugins/nf-hello/src/resources/META-INF/extensions.idx`
+
+    This file declares one or more extension classes provided by the plugin. 
+    Each line should contain a Java class fully qualified name implementing 
+    the interface `org.pf4j.ExtensionPoint` (or a sub-interface).
+
+- `plugins/nf-hello/src/main` 
+
+    The plugin implementation sources.
+
+- `plugins/nf-hello/src/test` 
+
+    The plugin unit tests. 
+
+## Compile & run unit tests 
+
+Run the following command in the project root directory (ie. where the file `settings.gradle` is located):
+
+    ./gradlew check
+
+## Run and debug plugin in the development environment
+
+To run and test the plugin in the development environment, configure a local Nextflow build 
+using the following steps:
+
+1. Clone the Nextflow repository in your computer into a sibling directory:
+
+    ```
+    git clone --depth 1 https://github.com/nextflow-io/nextflow ../nextflow
+    ```
+  
+2. Instruct the plugin build setting to use the local Nextflow code, adding the following 
+  line in the file `settings.gradle`: 
+   
+    ```
+    echo "includeBuild('../nextflow')" >> settings.gradle
+    ```
+  
+  (make sure to not add it more than once..)
+
+3. Compile the plugin along the Nextflow code, with this command:
+
+    ```
+    ./gradlew compileGroovy
+    ```
+
+4. Run Nextflow with plugins using the `./launch.sh` script as a drop-in replacement for the `nextflow` command and 
+  adding the option `-plugins nf-hello` to load the built plugin:
+   
+    ```
+    ./launch.sh run nextflow-io/hello -plugins nf-hello
+    ```
+
+## Package, upload and publish
+
+The project should hosted in a GitHub repository whose name should match the name of the plugin,
+that is the name of the directory in the `plugins` folder e.g. `nf-hello` in this project.
+
+Following these step to package, upload and publish the plugin:
+
+1. Create a file named `gradle.properties` in the project root containing the following attributes
+   (this file should not be committed in the project repository):
+
+  * `github_organization`: the GitHub organisation the plugin project is hosted
+  * `github_username` The GitHub username granting access to the plugin project.
+  * `github_access_token`:  The GitHub access token required to upload and commit changes in the plugin repository.
+  * `github_commit_email`:  The email address associated with your GitHub account.
+
+2. The following command, package and upload the plugin in the GitHub project releases page:
+
+    ```
+    ./gradlew :plugins:nf-hello:upload
+    ```
+
+3. Create a pull request against the [nextflow-io/plugins](https://github.com/nextflow-io/plugins/blob/main/plugins.json) 
+  project to make the plugin public accessible to Nextflow app. 
+