update Makefile and add option to compile and install to the plugins directory

Makefile

@@ -1,12 +1,16 @@
 
 config ?= compileClasspath
+version ?= $(shell grep 'Plugin-Version' plugins/nf-co2footprint/src/resources/META-INF/MANIFEST.MF | awk '{ print $$2 }')
 
 ifdef module 
 mm = :${module}:
 else 
 mm = 
 endif 
 
+NXF_HOME ?= $$HOME/.nextflow
+NXF_PLUGINS_DIR ?= $(NXF_HOME)/plugins
+
 clean:
 	./gradlew clean
 
@@ -44,6 +48,11 @@ else
 	./gradlew ${mm}test --tests ${class}
 endif
 
+install:
+	./gradlew copyPluginZip
+	rm -rf ${NXF_PLUGINS_DIR}/nf-co2footprint-${version}
+	cp -r build/plugins/nf-co2footprint-${version} ${NXF_PLUGINS_DIR}
+
 #
 # generate build zips under build/plugins
 # you can install the plugin copying manually these files to $HOME/.nextflow/plugins

docs/contributing/setup.md

@@ -59,6 +59,27 @@ To test with Nextflow for development purpose:
    ./launch.sh run -plugins nf-co2footprint <script/pipeline name> [pipeline params]
    ```
 
+## Alternative: Compile and install to Nextflow plugins directory
+
+!!! warning
+
+    This will install the compiled plugin code into your `$NXF_PLUGINS_DIR` directory (default: `${HOME}/.nextflow/plugins`). 
+    If the plugin version from the manifest file (`plugins/nf-co2footprint/src/resources/META-INF/MANIFEST.MF`) of the dev code matches an existing plugin, any install will be overwritten.
+
+1. Compile and install the plugin code
+
+   ```bash
+   make compile
+   make install
+   ```
+
+2. Run nextflow with this command, specifying the plugin version:
+
+   ```bash
+   nextflow run -plugins [email protected] <script/pipeline name> [pipeline params]
+   ```
+
+
 ## Change and preview the docs
 
 The docs are generated using [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/). To change the docs, edit the files in the [docs/](docs/) folder and run the following command to generate the docs (after installing mkdocs via `pip install mkdocs-material`):