From 8c1b2a34f2639ece2b15655af66b93dd8453aa75 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 18 Jul 2022 09:56:46 -0500
Subject: [PATCH] Add smart format selection to module

---
 modules/emboss/seqret/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/emboss/seqret/main.nf b/modules/emboss/seqret/main.nf
index 5dc3f397..12f7370c 100644
--- a/modules/emboss/seqret/main.nf
+++ b/modules/emboss/seqret/main.nf
@@ -21,13 +21,14 @@ process EMBOSS_SEQRET {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def osformat = args.contains('-osformat') ? '' : "-osformat ${out_ext}"
     """
     seqret \\
         ${args} \\
         -sequence ${sequence} \\
+        ${osformat} \\
         -outseq ${prefix}.${out_ext}
 
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         emboss: \$(echo \$(seqret -version 2>&1) | sed 's/EMBOSS://')