From 10df5608b6938af8c5f0363ddc515ad7e57a4454 Mon Sep 17 00:00:00 2001
From: Igor Trujnara <itrujnara@wp.pl>
Date: Wed, 8 Jan 2025 14:39:29 +0100
Subject: [PATCH] Add name safety, add compression to stub

---
 modules/nf-core/ripgrep/main.nf | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/ripgrep/main.nf b/modules/nf-core/ripgrep/main.nf
index 0c8eb16f70e..c283072ed9d 100644
--- a/modules/nf-core/ripgrep/main.nf
+++ b/modules/nf-core/ripgrep/main.nf
@@ -23,6 +23,9 @@ process RIPGREP {
     def args         = task.ext.args ?: ''
     def prefix       = task.ext.prefix ?: "${meta.id}"
     def write_output = compress ? " | pigz -cp ${task.cpus} > ${prefix}.txt.gz" : "> ${prefix}.txt"
+    if (!compress && files.contains("${prefix}.txt") || compress && files.contains("${prefix}.txt.gz")) {
+        error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    }
     """
     rg \\
         $args \\
@@ -40,8 +43,9 @@ process RIPGREP {
     stub:
     def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def write_output = compress ? "touch ${prefix}.txt.gz" : "touch ${prefix}.txt"
     """
-    touch ${prefix}.txt
+    $write_output
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":