Merge pull request #2546 from mashehu/fix-swf-linting-error

Fix swf test error

nf_core/__main__.py

@@ -1062,7 +1062,6 @@ def create_subworkflow(ctx, subworkflow, dir, author, force):
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
 @click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<nf-core/modules directory>")
-@click.option("-t", "--run-tests", is_flag=True, default=False, help="Run the test workflows")
 @click.option("-p", "--no-prompts", is_flag=True, default=False, help="Use defaults without prompting")
 @click.option("-u", "--update", is_flag=True, default=False, help="Update existing snapshots")
 @click.option("-o", "--once", is_flag=True, default=False, help="Run tests only once. Don't check snapshot stability")

nf_core/components/lint/__init__.py

@@ -10,7 +10,9 @@
 import os
 from pathlib import Path
 
-import rich
+import rich.box
+import rich.console
+import rich.panel
 from rich.markdown import Markdown
 from rich.table import Table
 
@@ -209,7 +211,7 @@ def _print_results(self, show_passed=False, sort_by="test"):
         self.failed.sort(key=operator.attrgetter(*sort_order))
 
         # Find maximum module name length
-        max_name_len = 40
+        max_name_len = len(self.component_type[:-1] + " name")
         for tests in [self.passed, self.warned, self.failed]:
             try:
                 for lint_result in tests:
@@ -264,7 +266,7 @@ def format_result(test_results, table):
             table = Table(style="yellow", box=rich.box.MINIMAL, pad_edge=False, border_style="dim")
             table.add_column(f"{self.component_type[:-1].title()} name", width=max_name_len)
             table.add_column("File path")
-            table.add_column("Test message")
+            table.add_column("Test message", overflow="fold")
             table = format_result(self.warned, table)
             console.print(
                 rich.panel.Panel(
@@ -278,10 +280,15 @@ def format_result(test_results, table):
 
         # Table of failing tests
         if len(self.failed) > 0:
-            table = Table(style="red", box=rich.box.MINIMAL, pad_edge=False, border_style="dim")
+            table = Table(
+                style="red",
+                box=rich.box.MINIMAL,
+                pad_edge=False,
+                border_style="dim",
+            )
             table.add_column(f"{self.component_type[:-1].title()} name", width=max_name_len)
             table.add_column("File path")
-            table.add_column("Test message")
+            table.add_column("Test message", overflow="fold")
             table = format_result(self.failed, table)
             console.print(
                 rich.panel.Panel(

nf_core/components/nfcore_component.py

@@ -4,6 +4,7 @@
 import logging
 import re
 from pathlib import Path
+from typing import Union
 
 log = logging.getLogger(__name__)
 
@@ -77,7 +78,7 @@ def __init__(
             self.test_yml = None
             self.test_main_nf = None
 
-    def _get_main_nf_tags(self, test_main_nf: str):
+    def _get_main_nf_tags(self, test_main_nf: Union[Path, str]):
         """Collect all tags from the main.nf.test file."""
         tags = []
         with open(test_main_nf, "r") as fh:
@@ -86,13 +87,19 @@ def _get_main_nf_tags(self, test_main_nf: str):
                     tags.append(line.strip().split()[1].strip('"'))
         return tags
 
-    def _get_included_components(self, main_nf: str):
+    def _get_included_components(self, main_nf: Union[Path, str]):
         """Collect all included components from the main.nf file."""
         included_components = []
         with open(main_nf, "r") as fh:
             for line in fh:
                 if line.strip().startswith("include"):
-                    included_components.append(line.strip().split()[-1].split(self.org)[-1].split("main")[0].strip("/"))
+                    # get tool/subtool or subworkflow name from include statement, can be in the form
+                    #'../../../modules/nf-core/hisat2/align/main'
+                    #'../bam_sort_stats_samtools/main'
+                    #'../subworkflows/nf-core/bam_sort_stats_samtools/main'
+                    component = line.strip().split()[-1].split(self.org)[-1].split("main")[0].strip("/")
+                    component = component.replace("'../", "subworkflows/")
+                    included_components.append(component)
         return included_components
 
     def get_inputs_from_main_nf(self):

nf_core/subworkflows/lint/subworkflow_tests.py

@@ -107,6 +107,7 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
             included_components = []
             if subworkflow.main_nf.is_file():
                 included_components = subworkflow._get_included_components(subworkflow.main_nf)
+            log.debug(f"Required tags: {required_tags}")
             missing_tags = []
             for tag in required_tags + included_components:
                 if tag not in main_nf_tags: