Merge pull request #3830 from mashehu/fix-ternary-containter-linting

fix ternary container linting

Author: mirpedrol

CHANGELOG.md

@@ -27,6 +27,7 @@
 - Use the org from .nf-core.yml when linting multiqc_config report_comment ([#3800](https://github.com/nf-core/tools/pull/3800))
 - Linting of patched subworkflows ([#3755](https://github.com/nf-core/tools/pull/3755))
 - Add link to modules and subworkflows linting error docs ([#3818](https://github.com/nf-core/tools/pull/3818))
+- fix ternary container linting ([#3830](https://github.com/nf-core/tools/pull/3830))
 
 ### Modules
 

nf_core/modules/lint/main_nf.py

@@ -314,11 +314,11 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
     # Deprecated enable_conda
     for i, raw_line in enumerate(lines):
         url = None
-        line = raw_line.strip(" \n'\"}:")
+        line = raw_line.strip(" \n'\"}:?")
 
         # Catch preceding "container "
         if line.startswith("container"):
-            line = line.replace("container", "").strip(" \n'\"}:")
+            line = line.replace("container", "").strip(" \n'\"}:?")
 
         if _container_type(line) == "conda":
             if "bioconda::" in line:
@@ -592,7 +592,7 @@ def check_process_labels(self, lines):
 def check_container_link_line(self, raw_line, registry):
     """Look for common problems in the container name / URL, for docker and singularity."""
 
-    line = raw_line.strip(" \n'\"}:")
+    line = raw_line.strip(" \n'\"}:?")
 
     # lint double quotes
     if line.count('"') > 2:

tests/modules/lint/test_main_nf.py

@@ -71,6 +71,15 @@ def test_process_labels(content, passed, warned, failed):
             0,
             1,
         ),
+        # Ternary with ? on next line (new Nextflow format) should pass
+        (
+            '''container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data'
+        : 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264'}"''',
+            6,
+            0,
+            0,
+        ),
     ],
 )
 def test_container_links(content, passed, warned, failed):