docs: add meta.strandedness to permitted meta keys

sites/docs/src/content/docs/developing/components/meta-map.md

@@ -31,12 +31,13 @@ A meta map sits in a tuple within a Nextflow channel object, next to the one or
 
 nf-core developers may define and within a pipelines or local subworkflows any name for a meta map key, and record any metadata they require for the execution of the pipeline.
 
-nf-core only defines 2 'standard' meta map keys.
+nf-core defines only two 'standard' meta map keys and one additional permitted key.
 
-| key               | purpose                                                                                          |
-| ----------------- | ------------------------------------------------------------------------------------------------ |
-| `meta.id`         | recording unique file identifiers associated with a file (e.g. 'sample' names in bioinformatics) |
-| `meta.single_end` | genomic sequencing pipelines handling paired-end sequencing data.                                |
+| key                 | purpose                                                                                          |
+| ------------------- | ------------------------------------------------------------------------------------------------ |
+| `meta.id`           | recording unique file identifiers associated with a file (e.g. 'sample' names in bioinformatics) |
+| `meta.single_end`   | genomic sequencing pipelines handling paired-end sequencing data.                                |
+| `meta.strandedness` | RNA-seq and other stranded library protocols. Permitted in modules, but not a standard key.      |
 
 There are no other standard or required key names that nf-core developers need to use.
 
@@ -47,11 +48,16 @@ No other 'standard' meta keys will be officially defined in the future.
 This is to provide maximum flexibility to pipeline developers.
 :::
 
+:::warning
+New modules SHOULD NOT use `meta.strandedness` directly. Use `ext.args` in `modules.config` instead.
+The only exception is sibling modules of a tool that already uses the pattern (e.g., RNA-seq alignment tools in the same family).
+:::
+
 ## Usage in nf-core components
 
 ### Modules
 
-The two standard meta map keys (`id` and `single_end`) are the [only keys allowed](../../specifications/components/modules/general#types-of-meta-fields) to be explicitly referred to in an nf-core/module.
+The keys `id`, `single_end`, and `strandedness` are the [only keys allowed](../../specifications/components/modules/general#types-of-meta-fields) to be explicitly referred to in an nf-core/module.
 
 nf-core/modules refer to meta maps in process `input:` blocks via an entry within a tuple.
 
@@ -82,7 +88,7 @@ All other usage of meta map keys within a module must come via the `ext.args` va
 
 ### Subworkflows
 
-No meta maps keys are to be assumed to be present in input channels other than the standard [key names](#key-names), similarly to [modules](#modules).
+No meta maps keys are to be assumed to be present in input channels beyond the [permitted key names](#key-names), similarly to [modules](#modules).
 
 In contrast to modules, nf-core/subworkflows are allowed to generate new meta map keys, that can be optionally emitted at the end of the subworkflow.
 

sites/docs/src/content/docs/specifications/components/modules/general.md

@@ -211,9 +211,14 @@ Meta variables SHOULD NOT use custom names.
 'Custom' hardcoded `meta` fields MUST NOT be used in modules.
 Do not refer to them within the module as expected input, nor generate new fields as output.
 
-The only accepted 'standard' meta map keys are `meta.id` or `meta.single_end`.
+The only accepted meta map keys are `meta.id`, `meta.single_end`, and `meta.strandedness`.
 Discuss proposals for other 'standard' fields for other disciplines with the maintainers team on slack under the [#modules channel](https://nfcore.slack.com/archives/CJRH30T6V).
 
+:::warning
+New modules SHOULD NOT use `meta.strandedness` directly. Use `ext.args` in `modules.config` instead.
+The only exception is sibling modules of a tool that already uses the pattern (e.g., RNA-seq alignment tools in the same family).
+:::
+
 :::info{title="Rationale" collapse}
 Write modules to allow as much flexibility to pipeline developers as possible.
 
@@ -226,7 +231,7 @@ In the module code DO NOT:
 ```nextflow title="main.nf"
 """script
 my_command \\
-  -r ${meta.strandedness} \\
+  -r ${meta.library_type} \\
   input.txt \\
   output.txt
 """
@@ -235,7 +240,7 @@ my_command \\
 ... but rather:
 
 ```groovy title="modules.conf"
-ext.args = { "-r ${meta.strandedness}" }
+ext.args = { "-r ${meta.library_type}" }
 ```
 
 And then in the module code:
@@ -258,17 +263,17 @@ However, once a module is included into a pipeline, they can be customised at th
 This can be performed with `nf-core modules patch`.
 If a hardcoded meta key name is an absolute necessity in a module, it MAY be incorporated and maintained with a patch file.
 
-In this example, `-r ${meta.strandedness}` is hardcoded in the `my_command` module.
+In this example, `-r ${meta.library_type}` is hardcoded in the `my_command` module.
 
 First install the tool into your pipeline with `nf-core modules install my_command`.
 
-Edit the `main.nf` to include `-r ${meta.strandedness}` and save it.
+Edit the `main.nf` to include `-r ${meta.library_type}` and save it.
 
 ```nextflow title="main.nf"
 script
 """
 my_command \\
-  -r ${meta.strandedness} \\
+  -r ${meta.library_type} \\
   ${args} \\
   input.txt \\
   output.txt