update version in ro crate on version bump

nf_core/pipelines/bump_version.py

@@ -11,6 +11,7 @@
 from ruamel.yaml import YAML
 
 import nf_core.utils
+from nf_core.pipelines.rocrate import ROCrate
 from nf_core.utils import Pipeline
 
 log = logging.getLogger(__name__)
@@ -127,6 +128,9 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
         yaml_key=["template", "version"],
     )
 
+    # update rocrate
+    ROCrate(pipeline_obj.wf_path).update_rocrate()
+
 
 def bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) -> None:
     """Bumps the required Nextflow version number of a pipeline.

nf_core/pipelines/rocrate.py

@@ -336,6 +336,28 @@ def add_main_authors(self, wf_file: rocrate.model.entity.Entity) -> None:
             if author in authors:
                 wf_file.append_to("maintainer", author_entitity)
 
+    def update_rocrate(self) -> bool:
+        """
+        Update the rocrate file
+        """
+        # check if we need to output a json file and/or a zip file based on the file extensions
+        json_path = None
+        zip_path = None
+        # try to find a json file
+        json_path = Path(self.pipeline_dir, "ro-crate-metadata.json")
+        if json_path.exists():
+            json_path = json_path
+        else:
+            json_path = None
+
+        # try to find a zip file
+        zip_path = Path(self.pipeline_dir, "ro-crate.crate.zip")
+        if zip_path.exists():
+            zip_path = zip_path
+        else:
+            zip_path = None
+        return self.create_rocrate(json_path=json_path, zip_path=zip_path)
+
 
 def get_orcid(name: str) -> Optional[str]:
     """

tests/pipelines/test_rocrate.py

@@ -1,5 +1,6 @@
 """Test the nf-core pipelines rocrate command"""
 
+import json
 import shutil
 import tempfile
 from pathlib import Path
@@ -12,6 +13,7 @@
 import nf_core.pipelines.create.create
 import nf_core.pipelines.rocrate
 import nf_core.utils
+from nf_core.pipelines.bump_version import bump_pipeline_version
 
 from ..test_pipelines import TestPipelines
 
@@ -125,3 +127,36 @@ def test_rocrate_creation_for_fetchngs(self):
 
         # Clean up
         shutil.rmtree(tmp_dir)
+
+    def test_update_rocrate(self):
+        """Run the nf-core rocrate command with a zip output"""
+
+        assert self.rocrate_obj.create_rocrate(json_path=self.pipeline_dir, zip_path=self.pipeline_dir)
+
+        # read the crate json file
+        with open(Path(self.pipeline_dir, "ro-crate-metadata.json")) as f:
+            crate = json.load(f)
+
+        # check the old version
+        self.assertEqual(crate["@graph"][2]["version"][0], "1.0.0dev")
+        # check creativeWorkStatus is InProgress
+        self.assertEqual(crate["@graph"][0]["creativeWorkStatus"], "InProgress")
+
+        # bump version
+        bump_pipeline_version(self.pipeline_obj, "1.1.0")
+
+        # Check that the crate was created
+        self.assertTrue(Path(self.pipeline_dir, "ro-crate.crate.zip").exists())
+
+        # Check that the crate was updated
+        self.assertTrue(Path(self.pipeline_dir, "ro-crate-metadata.json").exists())
+
+        # read the crate json file
+        with open(Path(self.pipeline_dir, "ro-crate-metadata.json")) as f:
+            crate = json.load(f)
+
+        # check that the version was updated
+        self.assertEqual(crate["@graph"][2]["version"][0], "1.1.0")
+
+        # check creativeWorkStatus is Stable
+        self.assertEqual(crate["@graph"][0]["creativeWorkStatus"], "Stable")