Merge pull request #6 from sanger-tol/cross-org-test

tests: Add test case for cross-organization subwf

tests/subworkflows/install.py

@@ -6,7 +6,9 @@
 from nf_core.subworkflows.install import SubworkflowInstall
 
 from ..utils import (
+    CROSS_ORGANIZATION_URL,
     GITLAB_BRANCH_TEST_BRANCH,
+    GITLAB_DEFAULT_BRANCH,
     GITLAB_REPO,
     GITLAB_SUBWORKFLOWS_BRANCH,
     GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH,
@@ -79,6 +81,19 @@ def test_subworkflows_install_different_branch_fail(self):
     assert install_obj.install("bam_stats_samtools") is False
 
 
+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, branch=GITLAB_DEFAULT_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
+    modules_json = ModulesJson(self.pipeline_dir)
+    mod_json = modules_json.get_modules_json()
+    assert mod_json["repos"][CROSS_ORGANIZATION_URL]["modules"]["jvfe"]["prokka"]["installed_by"] == [
+        "get_genome_annotation"
+    ]
+
+
 def test_subworkflows_install_tracking(self):
     """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json"""
     self.subworkflow_install.install("bam_sort_stats_samtools")

tests/test_subworkflows.py

@@ -120,6 +120,7 @@ def tearDown(self):
     )
     from .subworkflows.install import (  # type: ignore[misc]
         test_subworkflow_install_nopipeline,
+        test_subworkflows_install_across_organizations,
         test_subworkflows_install_alternate_remote,
         test_subworkflows_install_bam_sort_stats_samtools,
         test_subworkflows_install_bam_sort_stats_samtools_twice,

tests/utils.py

@@ -15,6 +15,7 @@
 OLD_TRIMGALORE_SHA = "9b7a3bdefeaad5d42324aa7dd50f87bea1b04386"
 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"
 GITLAB_REPO = "nf-core-test"
 GITLAB_DEFAULT_BRANCH = "main"
 GITLAB_SUBWORKFLOWS_BRANCH = "subworkflows"