From 30e534bc7eb58b7ea630e8496df7cb87a1bc96a1 Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Tue, 2 Jul 2024 16:57:43 +0100
Subject: [PATCH 1/2] Add comment about setting a default prefix that isn't
 just meta.id

---
 .../docs/src/content/docs/guidelines/components/modules.md | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/sites/docs/src/content/docs/guidelines/components/modules.md b/sites/docs/src/content/docs/guidelines/components/modules.md
index 687374ca8d..38b285767b 100644
--- a/sites/docs/src/content/docs/guidelines/components/modules.md
+++ b/sites/docs/src/content/docs/guidelines/components/modules.md
@@ -353,12 +353,17 @@ Channel names MUST follow `snake_case` convention and be all lower case.
 Output file (and/or directory) names SHOULD just consist of only `${prefix}` and the file-format suffix (e.g. `${prefix}.fq.gz` or `${prefix}.bam`).
 
 - This is primarily for re-usability so that other developers have complete flexibility to name their output files however they wish when using the same module.
-- As a result of using this syntax, if the module has the same named inputs and outputs then you can add a line in the `script` section like below (another example [here](https://github.com/nf-core/modules/blob/e20e57f90b6787ac9a010a980cf6ea98bd990046/modules/lima/main.nf#L37)) which will raise an error asking the developer to change the `args.prefix` variable to rename the output files so they don't clash.
+- As a result of using this syntax, if the module could _potentially_ have the same named inputs and outputs add a line in the `script` section like below (another example [here](https://github.com/nf-core/modules/blob/e20e57f90b6787ac9a010a980cf6ea98bd990046/modules/lima/main.nf#L37)) which will raise an error asking the developer to change the `args.prefix` variable to rename the output files so they don't clash.
 
   ```nextflow
   script:
   if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
   ```
+- If the input and output files are likely to have the same name, then an appropriate default prefix may be set, for example:
+
+  ```nextflow
+  def prefix = task.ext.prefix ?: "${meta.id}_sorted"
+  ```
 
 ## Input/output options
 

From 9eee363dc9ea0d25a75876c0668f18b261d2415a Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Tue, 2 Jul 2024 17:08:43 +0100
Subject: [PATCH 2/2] Update
 sites/docs/src/content/docs/guidelines/components/modules.md

---
 sites/docs/src/content/docs/guidelines/components/modules.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sites/docs/src/content/docs/guidelines/components/modules.md b/sites/docs/src/content/docs/guidelines/components/modules.md
index 38b285767b..5afdfaf230 100644
--- a/sites/docs/src/content/docs/guidelines/components/modules.md
+++ b/sites/docs/src/content/docs/guidelines/components/modules.md
@@ -359,6 +359,7 @@ Output file (and/or directory) names SHOULD just consist of only `${prefix}` and
   script:
   if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
   ```
+
 - If the input and output files are likely to have the same name, then an appropriate default prefix may be set, for example:
 
   ```nextflow