Add passthrough options for BCO

BCO.md

@@ -0,0 +1,147 @@
+# Additional BCO configuration
+
+The `bco` format supports additional "pass-through" options for certain BCO fields. These fields cannot be inferred automatically from a pipeline or run, and so must be entered through the config. External systems can use these config options to inject fields automatically.
+
+The following config options are supported:
+
+- `prov.formats.bco.provenance_domain.review`
+- `prov.formats.bco.provenance_domain.derived_from`
+- `prov.formats.bco.provenance_domain.obsolete_after`
+- `prov.formats.bco.provenance_domain.embargo`
+- `prov.formats.bco.usability_domain`
+- `prov.formats.bco.description_domain.keywords`
+- `prov.formats.bco.description_domain.xref`
+
+These options correspond exactly to fields in the BCO JSON schema. Refer to the [BCO User Guide](https://docs.biocomputeobject.org/user_guide/) for more information about these fields.
+
+Here is an example config based on the BCO User Guide:
+
+```groovy
+prov {
+  formats {
+    bco {
+      provenance_domain {
+        review = [
+          [
+            "status": "approved",
+            "reviewer_comment": "Approved by GW staff. Waiting for approval from FDA Reviewer",
+            "date": "2017-11-12T12:30:48-0400",
+            "reviewer": [
+              "name": "Charles Hadley King", 
+              "affiliation": "George Washington University", 
+              "email": "[email protected]",
+              "contribution": "curatedBy",
+              "orcid": "https://orcid.org/0000-0003-1409-4549"
+            ]
+          ],
+          [
+            "status": "approved",
+            "reviewer_comment": "The revised BCO looks fine",
+            "date": "2017-12-12T12:30:48-0400",
+            "reviewer": [
+              "name": "Eric Donaldson", 
+              "affiliation": "FDA", 
+              "email": "[email protected]",
+              "contribution": "curatedBy"
+            ]
+          ]
+        ]
+        derived_from = 'https://example.com/BCO_948701/1.0'
+        obsolete_after = '2118-09-26T14:43:43-0400'
+        embargo = [
+          "start_time": "2000-09-26T14:43:43-0400",
+          "end_time": "2000-09-26T14:43:45-0400"
+        ]
+      }
+      usability_domain = [
+        "Identify baseline single nucleotide polymorphisms (SNPs)[SO:0000694], (insertions)[SO:0000667], and (deletions)[SO:0000045] that correlate with reduced (ledipasvir)[pubchem.compound:67505836] antiviral drug efficacy in (Hepatitis C virus subtype 1)[taxonomy:31646]", 
+        "Identify treatment emergent amino acid (substitutions)[SO:1000002] that correlate with antiviral drug treatment failure", 
+        "Determine whether the treatment emergent amino acid (substitutions)[SO:1000002] identified correlate with treatment failure involving other drugs against the same virus", 
+        "GitHub CWL example: https://github.com/mr-c/hive-cwl-examples/blob/master/workflow/hive-viral-mutation-detection.cwl#L20"
+      ]
+      description_domain {
+        keywords = [
+          "HCV1a", 
+          "Ledipasvir", 
+          "antiviral resistance", 
+          "SNP", 
+          "amino acid substitutions"
+        ]
+        xref = [
+          [
+            "namespace": "pubchem.compound",
+            "name": "PubChem-compound",
+            "ids": ["67505836"], 
+            "access_time": "2018-13-02T10:15-05:00"
+          ],
+          [
+            "namespace": "pubmed",
+            "name": "PubMed",
+            "ids": ["26508693"], 
+            "access_time": "2018-13-02T10:15-05:00"
+          ],
+          [
+            "namespace": "so",
+            "name": "Sequence Ontology",
+            "ids": ["SO:000002", "SO:0000694", "SO:0000667", "SO:0000045"],
+            "access_time": "2018-13-02T10:15-05:00"
+          ],
+          [
+            "namespace": "taxonomy",
+            "name": "Taxonomy",
+            "ids": ["31646"], 
+            "access_time": "2018-13-02T10:15-05:00"
+          ]
+        ]
+      }
+    }
+  }
+}
+```
+
+Alternatively, you can use params to make it easier for an external system:
+
+```groovy
+prov {
+  formats {
+    bco {
+      provenance_domain {
+        review = params.bco_provenance_domain_review
+        derived_from = params.bco_provenance_domain_derived_from
+        obsolete_after = params.bco_provenance_domain_obsolete_after
+        embargo = params.bco_provenance_domain_embargo
+      }
+      usability_domain = params.bco_usability_domain
+      description_domain {
+        keywords = params.bco_description_domain_keywords
+        xref = params.bco_description_domain_xref
+      }
+    }
+  }
+}
+```
+
+This way, the pass-through options can be provided as JSON in a [params file](https://nextflow.io/docs/latest/reference/cli.html#run):
+
+```jsonc
+{
+    "bco_provenance_domain_review": [
+        // ...
+    ],
+    "derived_from": "...",
+    "obsolete_after": "...",
+    "embargo": {
+        "start_time": "...",
+        "end_time": "..."
+    },
+    "bco_usability_domain": [
+        // ...
+    ],
+    "bco_description_domain_keywords": [
+        // ...
+    ],
+    "bco_description_domain_xref": [
+        // ...
+    ]
+}
+```

README.md

@@ -44,7 +44,7 @@ Configuration scope for the desired output formats. The following formats are av
 
 - `bco`: Render a [BioCompute Object](https://biocomputeobject.org/). Supports the `file` and `overwrite` options.
 
-  Visit the [BCO User Guide](https://docs.biocomputeobject.org/user_guide/) to learn more about this format and how to extend it with information that isn't available to Nextflow.
+  *New in version 1.3.0*: additional "pass-through" options are available for BCO fields that can't be inferred from the pipeline. See [BCO.md](./BCO.md) for more information.
 
 - `dag`: Render the task graph as a Mermaid diagram embedded in an HTML document. Supports the `file` and `overwrite` options.
 

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

@@ -67,6 +67,15 @@ class BcoRenderer implements Renderer {
         final nextflowVersion = nextflowMeta.version.toString()
         final params = session.config.params as Map
 
+        final config = session.config
+        final review            = config.navigate('prov.formats.bco.provenance_domain.review', []) as List<Map<String,?>>
+        final derived_from      = config.navigate('prov.formats.bco.provenance_domain.derived_from') as String
+        final obsolete_after    = config.navigate('prov.formats.bco.provenance_domain.obsolete_after') as String
+        final embargo           = config.navigate('prov.formats.bco.provenance_domain.embargo') as Map<String,String>
+        final usability         = config.navigate('prov.formats.bco.usability_domain', []) as List<String>
+        final keywords          = config.navigate('prov.formats.bco.description_domain.keywords', []) as List<String>
+        final xref              = config.navigate('prov.formats.bco.description_domain.xref', []) as List<Map<String,?>>
+
         // create BCO manifest
         final bco = [
             "object_id": null,
@@ -75,6 +84,9 @@ class BcoRenderer implements Renderer {
             "provenance_domain": [
                 "name": manifest.name ?: "",
                 "version": manifest.version ?: "",
+                "review": review,
+                "obsolete_after": obsolete_after,
+                "embargo": embargo,
                 "created": dateCreated,
                 "modified": dateCreated,
                 "contributors": authors.collect( name -> [
@@ -83,10 +95,11 @@ class BcoRenderer implements Renderer {
                 ] ),
                 "license": ""
             ],
-            "usability_domain": [],
+            "usability_domain": usability,
             "extension_domain": [],
             "description_domain": [
-                "keywords": [],
+                "keywords": keywords,
+                "xref": xref,
                 "platform": ["Nextflow"],
                 "pipeline_steps": tasks.sort( (task) -> task.id ).collect { task -> [
                     "step_number": task.id,