feat: Allow defining branches in meta.yml

nf_core/components/components_utils.py

@@ -174,6 +174,7 @@ def get_components_to_install(subworkflow_dir: str) -> Tuple[List[Dict[str, Opti
                             "name": name,
                             "org_path": org_path,
                             "git_remote": git_remote,
+                            "branch": component[name].get("branch", "master"),
                         }
                     component_list.append(comp_dict)
             modules = component_list

nf_core/components/install.py

@@ -58,7 +58,8 @@ def install(self, component, silent=False):
         if isinstance(component, dict):
             if component["git_remote"] is not None:
                 remote_url = component["git_remote"]
-                self.modules_repo = ModulesRepo(remote_url, self.branch)
+                branch = component["branch"]
+                self.modules_repo = ModulesRepo(remote_url, branch)
             else:
                 self.modules_repo = ModulesRepo(self.current_remote, self.branch)
             component = component["name"]

tests/subworkflows/install.py

@@ -6,6 +6,7 @@
 from nf_core.subworkflows.install import SubworkflowInstall
 
 from ..utils import (
+    CROSS_ORGANIZATION_BRANCH,
     CROSS_ORGANIZATION_URL,
     GITLAB_BRANCH_TEST_BRANCH,
     GITLAB_REPO,
@@ -82,7 +83,9 @@ def test_subworkflows_install_different_branch_fail(self):
 
 def test_subworkflows_install_across_organizations(self):
     """Test installing a subworkflow with modules from different organizations"""
-    install_obj = SubworkflowInstall(self.pipeline_dir, remote_url=CROSS_ORGANIZATION_URL)
+    install_obj = SubworkflowInstall(
+        self.pipeline_dir, remote_url=CROSS_ORGANIZATION_URL, branch=CROSS_ORGANIZATION_BRANCH
+    )
     # The hic_bwamem2 subworkflow contains modules from different organizations
     install_obj.install("get_genome_annotation")
     # Verify that the installed_by entry was added correctly

tests/utils.py

@@ -17,6 +17,7 @@
 OLD_TRIMGALORE_BRANCH = "mimic-old-trimgalore"
 GITLAB_URL = "https://gitlab.com/nf-core/modules-test.git"
 CROSS_ORGANIZATION_URL = "https://github.com/jvfe/test-subworkflow-remote.git"
+CROSS_ORGANIZATION_BRANCH = "main"
 GITLAB_REPO = "nf-core-test"
 GITLAB_DEFAULT_BRANCH = "main"
 GITLAB_SUBWORKFLOWS_BRANCH = "subworkflows"