Add Workflow Run RO-crate format

README.md

@@ -26,7 +26,7 @@ prov {
 }
 ```
 
-Finally, run your Nextflow pipeline. You do not need to modify your pipeline script in order to use the `nf-prov` plugin. The plugin will automatically generate a JSON file with provenance information.
+Finally, run your Nextflow pipeline. You do not need to modify your pipeline script in order to use the `nf-prov` plugin. The plugin will automatically produce the specified provenance reports at the end of the workflow run.
 
 ## Configuration
 
@@ -52,6 +52,10 @@ Configuration scope for the desired output formats. The following formats are av
 
 - `legacy`: Render the legacy format originally defined in this plugin (default). Supports the `file` and `overwrite` options.
 
+*New in version 1.4.0*
+
+- `wrroc`: Render a [Workflow Run RO-Crate](https://www.researchobject.org/workflow-run-crate/). Includes all three profiles (Process, Workflow, and Provenance).
+
 Any number of formats can be specified, for example:
 
 ```groovy
@@ -69,6 +73,8 @@ prov {
 }
 ```
 
+See [nextflow.config](./nextflow.config) for a full example of each provenance format.
+
 `prov.patterns`
 
 List of file patterns to include in the provenance report, from the set of published files. By default, all published files are included.
@@ -114,16 +120,16 @@ Following these step to package, upload and publish the plugin:
 
 2. Update the `Plugin-Version` field in the following file with the release version:
 
-    ```bash
-    plugins/nf-prov/src/resources/META-INF/MANIFEST.MF
-    ```
+   ```bash
+   plugins/nf-prov/src/resources/META-INF/MANIFEST.MF
+   ```
 
 3. Run the following command to package and upload the plugin in the GitHub project releases page:
 
-    ```bash
-    ./gradlew :plugins:nf-prov:upload
-    ```
+   ```bash
+   ./gradlew :plugins:nf-prov:upload
+   ```
 
-4. 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. 
+4. 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.
 

nextflow.config

@@ -20,5 +20,29 @@ prov {
             file = "${params.outdir}/manifest.json"
             overwrite = true
         }
+        wrroc {
+            file = "${params.outdir}/ro-crate-metadata.json"
+            overwrite = true
+            agent {
+                name = "John Doe"
+                orcid = "https://orcid.org/0000-0000-0000-0000"
+                email = "[email protected]"
+                phone = "(0)89-99998 000"
+                contactType = "Researcher"
+            }
+            organization {
+                name = "University of XYZ"
+                ror = "https://ror.org/000000000"
+                isPublisher = true
+            }
+            publisher {
+                id = "https://ror.org/000000000"
+            }
+            profile = "provenance_run_crate"
+        }
     }
 }
+
+manifest {
+    license = "https://spdx.org/licenses/Apache-2.0"
+}

plugins/nf-prov/src/main/nextflow/prov/ProvObserver.groovy

@@ -40,7 +40,7 @@ import nextflow.trace.TraceRecord
 @CompileStatic
 class ProvObserver implements TraceObserver {
 
-    public static final List<String> VALID_FORMATS = ['bco', 'dag', 'legacy']
+    public static final List<String> VALID_FORMATS = ['bco', 'dag', 'legacy', 'wrroc']
 
     private Session session
 
@@ -71,6 +71,9 @@ class ProvObserver implements TraceObserver {
         if( name == 'legacy' )
             return new LegacyRenderer(opts)
 
+        if( name == 'wrroc' )
+            return new WrrocRenderer(opts)
+
         throw new IllegalArgumentException("Invalid provenance format -- valid formats are ${VALID_FORMATS.join(', ')}")
     }