add EDAM comments and suggestions from review

nf_core/components/components_utils.py

@@ -196,10 +196,13 @@ def get_biotools_id(data: dict, tool_name: str) -> str:
     log.warning(f"Could not find a bio.tools ID for '{tool_name}'")
     return ""
 
-type DictWithListAndStr = Dict[str, Tuple[List[str], str]]
+
+type DictWithStrAndTuple = Dict[str, Tuple[List[str], List[str]]]
+
+
 def get_channel_info_from_biotools(
     data: dict, tool_name: str
-) -> Optional[Tuple[DictWithListAndStr, DictWithListAndStr]] :
+) -> Optional[Tuple[DictWithStrAndTuple, DictWithStrAndTuple]]:
     """
     Try to find input and output channels and the respective EDAM ontology terms
 
@@ -210,24 +213,21 @@ def get_channel_info_from_biotools(
     inputs = {}
     outputs = {}
 
-    def _iterate_input_output(type) -> DictWithListAndStr:
+    def _iterate_input_output(type) -> DictWithStrAndTuple:
         type_info = {}
         if type in funct:
             for element in funct[type]:
                 if "data" in element:
                     element_name = "_".join(element["data"]["term"].lower().split(" "))
                     uris = [element["data"]["uri"]]
-                    terms = ""
+                    terms = [""]
                 if "format" in element:
                     for format in element["format"]:
                         # Append the EDAM URI
                         uris.append(format["uri"])
                         # Append the EDAM term, getting the first word in case of complicated strings. i.e. "FASTA format"
-                        terms = terms + format["term"].lower().split(" ")[0] + ","
-                    type_info[element_name] = (
-                        uris,
-                        terms[:-1],  # Remove the last comma
-                    )
+                        terms.append(format["term"].lower().split(" ")[0])
+                    type_info[element_name] = (uris, terms)
         return type_info
 
     # Iterate through the tools in the response to find the tool name

nf_core/module-template/environment.yml

@@ -4,4 +4,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  # TODO nf-core: List required Conda package(s).
+  #               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+  #               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
   - "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}"

nf_core/module-template/main.nf

@@ -22,9 +22,6 @@ process {{ component_name_underscore|upper }} {
     label '{{ process_label }}'
 
     {% if not_empty_template -%}
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     {% endif -%}
     conda "${moduleDir}/environment.yml"
@@ -34,7 +31,7 @@ process {{ component_name_underscore|upper }} {
 
     input:
     {%- if inputs %}
-    // TODO nf-core: Update the information obtained form bio.tools and make sure that it is correct
+    // TODO nf-core: Update the information obtained from bio.tools and make sure that it is correct
     {%- for input_name, ontologies in inputs.items() %}
     {{ 'tuple val(meta), path(' + input_name + ')' if has_meta else 'path ' + input_name }}
     {%- endfor %}
@@ -54,9 +51,9 @@ process {{ component_name_underscore|upper }} {
 
     output:
     {%- if outputs %}
-    // TODO nf-core: Update the information obtained form bio.tools and make sure that it is correct
+    // 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[1] + '}")' if has_meta else 'path ' + output_name }}, emit: {{ output_name }}
+    {{ 'tuple val(meta), path("*{' + ontologies[1]|join(',') + '}")' if has_meta else 'path ' + output_name }}, emit: {{ output_name }}
     {%- endfor %}
     {%- else %}
     {% if not_empty_template -%}
@@ -96,7 +93,7 @@ process {{ component_name_underscore|upper }} {
         {%- if has_meta %}
         {%- if inputs %}
         {%- for input_name, ontologies in inputs.items() %}
-        {%- set extensions = ontologies[1].split(',') %}
+        {%- set extensions = ontologies[1] %}
         {%- for ext in extensions %}
         -o ${prefix}.{{ ext }} \\
         {%- endfor %}
@@ -135,7 +132,7 @@ process {{ component_name_underscore|upper }} {
     {% if not_empty_template -%}
     {%- if inputs %}
     {%- for input_name, ontologies in inputs.items() %}
-    {%- set extensions = ontologies[1].split(',') %}
+    {%- set extensions = ontologies[1] %}
     {%- for ext in extensions %}
     touch ${prefix}.{{ ext }}
     {%- endfor %}

nf_core/module-template/meta.yml

@@ -33,16 +33,16 @@ input:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. `[ id:'sample1', single_end:false ]`
+          e.g. `[ id:'sample1' ]`
   {% endif %}
     - {{ input_name }}:
-        # TODO nf-core: Update the information obtained form bio.tools and make sure that it is correct
+        # TODO nf-core: Update the information obtained from bio.tools and make sure that it is correct
         type: file
         description: {{ input_name }} file
-        pattern: {{ "\"*.{" + ontologies[1] + "}\"" }}
+        pattern: {{ "\"*.{" + ontologies[1]|join(",") + "}\"" }}
         ontologies:
           {% for ontology in ontologies[0] -%}
-          - edam: "{{ ontology }}"
+          - edam: "{{ ontology }}" # {{ ontologies[1][loop.index0] }}
           {% endfor -%}
   {% endfor -%}
   {% else -%}
@@ -51,7 +51,7 @@ input:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. `[ id:'sample1', single_end:false ]`
+          e.g. `[ id:'sample1' ]`
   {% endif %}
   {% if not_empty_template -%}
   ## TODO nf-core: Delete / customise this example input
@@ -82,16 +82,16 @@ output:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. `[ id:'sample1', single_end:false ]`
+          e.g. `[ id:'sample1' ]`
     {%- endif %}
     - {{ output_name }}:
-        # TODO nf-core: Update the information obtained form bio.tools and make sure that it is correct
+        # TODO nf-core: Update the information obtained from bio.tools and make sure that it is correct
         type: file
         description: {{ output_name }} file
-        pattern: {{ "\"*.{" + ontologies[1] + "}\"" }}
+        pattern: {{ "\"*.{" + ontologies[1]|join(",") + "}\"" }}
         ontologies:
           {%- for ontology in ontologies[0] %}
-          - edam: "{{ ontology }}"
+          - edam: "{{ ontology }}" # {{ ontologies[1][loop.index0] }}
           {%- endfor %}
   {% endfor -%}
   {% else -%}
@@ -101,7 +101,7 @@ output:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. `[ id:'sample1', single_end:false ]`
+          e.g. `[ id:'sample1' ]`
   {%- endif %}
   {% if not_empty_template -%}
     ## TODO nf-core: Delete / customise this example output

tests/components/test_components_utils.py

@@ -36,13 +36,13 @@ def test_get_biotools_ch_info(self):
                         "http://edamontology.org/format_2182",
                         "http://edamontology.org/format_2573",
                     ],
-                    "fastq-like,sam",
+                    ["fastq-like", "sam"],
                 )
             }
             assert outputs == {
                 "sequence_report": (
                     ["http://edamontology.org/data_2955", "http://edamontology.org/format_2331"],
-                    "html",
+                    ["html"],
                 )
             }