add subworfklow + schema for references (#7412)

* add subworfklow + schema for references

* s3 -> https

* no function tests

* better function name

* restore fake workflow for tests

* add DISCLAIMER

* better tests

* use format: path

subworkflows/nf-core/utils_references/README.md

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+# Disclaimer
+
+This `utils_references/` folder contains for now two functions and a schema.
+This is really meant for a POC and should not be installed by anyone except @maxulysse.
+But that was the easiest way to share functions and a schema between three different pipelines and still showcase the logic.
+This might evolve in the future, possibly towards a proper plugin.
+
+If you do so, please be aware that:
+
+- @maxulysse has hacked the `main.nf` to test the functions and the schema
+- This is really meant to evolve in the future and can be deleted at any moment without prior notice.
+
+That being said, if you still want to use it or want to know more about it, please check the `#references` channel on the nf-core slack.

subworkflows/nf-core/utils_references/main.nf

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+// DISCLAIMER:
+// This subworkflow is just to test the functions and the schema
+// It should not be used in any pipeline
+
+// This include statement can also be deleted
+include { samplesheetToList } from 'plugin/nf-schema'
+
+workflow UTILS_REFERENCES {
+    take:
+    yaml_reference
+    param_file
+    param_value
+    attribute_file
+    attribute_value
+    basepath
+
+    main:
+    references = Channel.fromList(samplesheetToList(yaml_reference, "${projectDir}/subworkflows/nf-core/utils_references/schema_references.json"))
+
+    // GIVING up writing a test for the functions, so writing a subworkflow to test it
+    references_file = get_references_file(references, param_file, attribute_file, basepath)
+    references_value = get_references_value(references, param_value, attribute_value)
+
+    emit:
+    references_file
+    references_value
+}
+// You can delete everything before this line (including this line)
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    FUNCTIONS TO EXTRACT REFERENCES FILES OR VALUES FROM THE REFERENCES YAML OR PARAMS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+def get_references_file(references, param, attribute, basepath) {
+    return references
+        .map { meta, _readme ->
+            if (param || meta[attribute]) {
+                [meta.subMap(['id']), file(param ?: meta[attribute].replace('${params.igenomes_base}', basepath), checkIfExists: true)]
+            }
+            else {
+                null
+            }
+        }
+        .collect()
+}
+
+def get_references_value(references, param, attribute) {
+    return references
+        .map { meta, _readme ->
+            if (param || meta[attribute]) {
+                [meta.subMap(['id']), param ?: meta[attribute]]
+            }
+            else {
+                null
+            }
+        }
+        .collect()
+}

subworkflows/nf-core/utils_references/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "utils_references"
+description: Functionality for dealing with references that may be useful for any Nextflow pipeline
+keywords:
+  - utility
+  - pipeline
+  - references
+components: []
+input: []
+output: []
+authors:
+  - "@maxulysse"
+maintainers:
+  - "@maxulysse"