From 7de971b2a84fe46cfa3982727f09b9e2916b3d59 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 24 Jul 2025 13:20:41 +0200
Subject: [PATCH 1/2] poc with samtools/sort

---
 modules/nf-core/samtools/sort/main.nf | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index caf3c61a87d..e1858868105 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -1,6 +1,7 @@
 process SAMTOOLS_SORT {
     tag "$meta.id"
     label 'process_medium'
+    ext prefix: "${meta.id}", args: '', when: true
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -18,12 +19,11 @@ process SAMTOOLS_SORT {
     tuple val(meta), path("*.csi"),  emit: csi,  optional: true
     path  "versions.yml",            emit: versions
 
-    when:
-    task.ext.when == null || task.ext.when
+    when: task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args
+    def prefix = task.ext.prefix
     def extension = args.contains("--output-fmt sam") ? "sam" :
                     args.contains("--output-fmt cram") ? "cram" :
                     "bam"
@@ -49,8 +49,8 @@ process SAMTOOLS_SORT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args
+    def prefix = task.ext.prefix
     def extension = args.contains("--output-fmt sam") ? "sam" :
                     args.contains("--output-fmt cram") ? "cram" :
                     "bam"

From 311bd0a1f828091d7dee3e033e83593de8ceb158 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 24 Jul 2025 13:28:09 +0200
Subject: [PATCH 2/2] use smoove as another example

---
 modules/nf-core/smoove/call/main.nf | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/smoove/call/main.nf b/modules/nf-core/smoove/call/main.nf
index 7c5774c59ce..ab76587f2d3 100644
--- a/modules/nf-core/smoove/call/main.nf
+++ b/modules/nf-core/smoove/call/main.nf
@@ -1,6 +1,7 @@
 process SMOOVE_CALL {
     tag "$meta.id"
     label 'process_high'
+    ext prefix: "${meta.id}", args: '', when: true
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -16,12 +17,11 @@ process SMOOVE_CALL {
     tuple val(meta), path("*.vcf.gz"), emit: vcf
     path "versions.yml"              , emit: versions
 
-    when:
-    task.ext.when == null || task.ext.when
+    when: task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args
+    def prefix = task.ext.prefix
 
     def exclude = exclude_beds ? "--exclude ${exclude_beds}" : ""
     """
@@ -41,7 +41,7 @@ process SMOOVE_CALL {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix
     """
     echo "" | gzip > ${prefix}.vcf.gz