fix more pytests

nf-core · Feb 11, 2025 · 47036ff · 47036ff
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commit 47036ff
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Showing 3 changed files with 6 additions and 4 deletions.
diff --git a/nf_core/module-template/main.nf b/nf_core/module-template/main.nf
@@ -53,7 +53,7 @@ process {{ component_name_underscore|upper }} {
     {%- if outputs %}
     // TODO nf-core: Update the information obtained from bio.tools and make sure that it is correct
     {%- for output_name, ontologies in outputs.items() %}
-    {{ 'tuple val(meta), path("*{' + ontologies[2]|join(',') + '}")' if has_meta else 'path ' + output_name }}, emit: {{ output_name }}
+    {{ 'tuple val(meta), path("*.{' + ontologies[2]|join(',') + '}")' if has_meta else 'path ' + output_name }}, emit: {{ output_name }}
     {%- endfor %}
     {%- else %}
     {% if not_empty_template -%}

diff --git a/tests/components/test_components_utils.py b/tests/components/test_components_utils.py
@@ -36,13 +36,15 @@ def test_get_biotools_ch_info(self):
                         "http://edamontology.org/format_2182",
                         "http://edamontology.org/format_2573",
                     ],
-                    ["", "fastq-like", "sam"],
+                    ["Raw sequence", "FASTQ-like format (text)", "SAM"],
+                    ["fastq-like", "sam"],
                 )
             }
             assert outputs == {
                 "sequence_report": (
                     ["http://edamontology.org/data_2955", "http://edamontology.org/format_2331"],
-                    ["", "html"],
+                    ["Sequence report", "HTML"],
+                    ["html"],
                 )
             }
 

diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py
@@ -526,7 +526,7 @@ def test_modules_meta_yml_output_mismatch(self):
         """Test linting a module with an extra entry in output fields in meta.yml compared to module.output"""
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh:
             main_nf = fh.read()
-        main_nf_new = main_nf.replace("emit: bam", "emit: bai")
+        main_nf_new = main_nf.replace("emit: sequence_report", "emit: bai")
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
             fh.write(main_nf_new)
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)