Merge branch 'dev' into fix/1927

* dev:
  only add entry to files
  remove remaining print
  [automated] Update CHANGELOG.md
  fix edam BAM link on modules template
  add ontologies to meta.yml if not present
  [automated] Update CHANGELOG.md
  [automated] Update CHANGELOG.md
  docs: fix contributing link in the main README
  fix: linting with comments after the input directive

Author: jvfe

CHANGELOG.md

@@ -10,6 +10,8 @@
 ### Linting
 
 - 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
 
@@ -26,6 +28,7 @@
 - Update prettier to 3.5.0 ([#3448](https://github.com/nf-core/tools/pull/3448))
 - chore(deps): update python:3.12-slim docker digest to 34656cd ([#3450](https://github.com/nf-core/tools/pull/3450))
 - Remove Twitter from README ([#3454](https://github.com/nf-core/tools/pull/3454))
+- docs: fix contributing link in the main README ([#3459](https://github.com/nf-core/tools/pull/3459))
 - Continuation of #3083 ([#3456](https://github.com/nf-core/tools/pull/3456))
 
 ## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]

README.md

@@ -61,7 +61,7 @@ pip install --upgrade -r requirements-dev.txt -e .
 
 ## Contributions and Support
 
-If you would like to contribute to this package, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+If you would like to contribute to this package, please see the [contributing guidelines](CONTRIBUTING.md).
 
 For further information or help, don't hesitate to get in touch on the [Slack `#tools` channel](https://nfcore.slack.com/channels/tools) (you can join with [this invite](https://nf-co.re/join/slack)).
 

nf_core/components/nfcore_component.py

@@ -206,6 +206,7 @@ def get_inputs_from_main_nf(self) -> None:
             input_data = data.split("input:")[1].split("output:")[0]
             for line in input_data.split("\n"):
                 channel_elements: Any = []
+                line = line.split("//")[0]  # remove any trailing comments
                 regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
                 matches = re.finditer(regex, line)
                 for _, match in enumerate(matches, start=1):

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: