From ed78ba7ec74aecdcce4ff3e49910ceef98f33708 Mon Sep 17 00:00:00 2001
From: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Thu, 3 Oct 2024 12:25:08 +0000
Subject: [PATCH] Cutadapt: fix non-functional action parameter

---
 CHANGELOG.md           | 4 ++++
 src/cutadapt/script.sh | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a2aa5387..e5b6f7b9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,10 @@
 
 * `falco`: Fix a typo in the `--reverse_complement` argument (PR #157).
 
+## BUG FIXES
+
+* `cutadapt`: fix the the non-functional `action` parameter (PR #).
+
 ## MINOR CHANGES
 
 * Upgrade to Viash 0.9.0.
diff --git a/src/cutadapt/script.sh b/src/cutadapt/script.sh
index 20c92724..d181e2b0 100644
--- a/src/cutadapt/script.sh
+++ b/src/cutadapt/script.sh
@@ -108,7 +108,7 @@ input_args=$(echo \
   ${par_overlap:+--overlap "${par_overlap}"} \
   ${par_match_read_wildcards:+--match-read-wildcards} \
   ${par_no_match_adapter_wildcards:+--no-match-adapter-wildcards} \
-  ${par_action:+--action "${par_action}"} \
+  ${par_action:+--action="${par_action}"} \
   ${par_revcomp:+--revcomp} \
 )
 debug "Arguments to cutadapt:"