Merge pull request #3460 from mirpedrol/edam-ontology-fixes

Linting: EDAM ontology fixes

Author: mirpedrol

CHANGELOG.md

@@ -11,6 +11,7 @@
 
 - Add linting for ifEmpty(null) ([#3411](https://github.com/nf-core/tools/pull/3411))
 - fix: linting with comments after the input directive ([#3458](https://github.com/nf-core/tools/pull/3458))
+- EDAM ontology fixes ([#3460](https://github.com/nf-core/tools/pull/3460))
 
 ### Modules
 

nf_core/module-template/meta.yml

@@ -62,7 +62,7 @@ input:
         pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }}
         ontologies:
           {% if not_empty_template -%}
-          - edam: "http://edamontology.org/format_25722" # BAM
+          - edam: "http://edamontology.org/format_2572" # BAM
           - edam: "http://edamontology.org/format_2573" # CRAM
           - edam: "http://edamontology.org/format_3462" # SAM
           {% else -%}
@@ -112,7 +112,7 @@ output:
         pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }}
         ontologies:
           {% if not_empty_template -%}
-          - edam: "http://edamontology.org/format_25722" # BAM
+          - edam: "http://edamontology.org/format_2572" # BAM
           - edam: "http://edamontology.org/format_2573" # CRAM
           - edam: "http://edamontology.org/format_3462" # SAM
           {% else -%}

nf_core/modules/lint/__init__.py

@@ -394,6 +394,8 @@ def update_meta_yml_file(self, mod):
                     if "ontologies" in corrected_meta_yml["input"][i][j][element_name]:
                         for ontology in corrected_meta_yml["input"][i][j][element_name]["ontologies"]:
                             current_ontologies_i.append(ontology["edam"])
+                    elif corrected_meta_yml["input"][i][j][element_name]["type"] == "file":
+                        corrected_meta_yml["input"][i][j][element_name]["ontologies"] = []
                     log.debug(f"expected ontologies for input: {expected_ontologies_i}")
                     log.debug(f"current ontologies for input: {current_ontologies_i}")
                     for ontology, ext in expected_ontologies_i:
@@ -404,7 +406,6 @@ def update_meta_yml_file(self, mod):
                             corrected_meta_yml["input"][i][j][element_name]["ontologies"][-1].yaml_add_eol_comment(
                                 f"{edam_formats[ext][1]}", "edam"
                             )
-                            print(f"added comment {edam_formats[ext][1]}")
         if "output" in meta_yml:
             for i, channel in enumerate(corrected_meta_yml["output"]):
                 ch_name = list(channel.keys())[0]
@@ -420,6 +421,8 @@ def update_meta_yml_file(self, mod):
                     if "ontologies" in corrected_meta_yml["output"][i][ch_name][j][element_name]:
                         for ontology in corrected_meta_yml["output"][i][ch_name][j][element_name]["ontologies"]:
                             current_ontologies_o.append(ontology["edam"])
+                    elif corrected_meta_yml["output"][i][ch_name][j][element_name]["type"] == "file":
+                        corrected_meta_yml["output"][i][ch_name][j][element_name]["ontologies"] = []
                     log.debug(f"expected ontologies for output: {expected_ontologies_o}")
                     log.debug(f"current ontologies for output: {current_ontologies_o}")
                     for ontology, ext in expected_ontologies_o: