lint all components recursively in test.yml tags

nf_core/subworkflows/lint/subworkflow_tests.py

@@ -3,6 +3,7 @@
 """
 import logging
 import os
+from pathlib import Path
 
 import yaml
 
@@ -53,7 +54,7 @@ def subworkflow_tests(_, subworkflow):
  with open(subworkflow.test_yml, "r") as fh:
  test_yml = yaml.safe_load(fh)
 
- # Verify that tags are correct
+ # Verify that tags are correct. All included components in test main.nf should be specified in test.yml so pytests run for all of them
  included_components = nf_core.subworkflows.SubworkflowTestYmlBuilder.parse_module_tags(
  subworkflow, subworkflow.component_dir
  )
@@ -75,6 +76,12 @@ def subworkflow_tests(_, subworkflow):
  subworkflow.test_yml,
  )
  )
+ if component.startswith("subworkflows/"):
+ included_components += nf_core.subworkflows.SubworkflowTestYmlBuilder.parse_module_tags(
+ _,
+ Path(subworkflow.component_dir).parent.joinpath(component.replace("subworkflows/", "")),
+ )
+ included_components = list(set(included_components))
 
  # Look for md5sums of empty files
  for tfile in test.get("files", []):