From 51d656555f9635bb8988f9eec904ee66657736e1 Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Wed, 19 Apr 2023 09:52:31 +0200
Subject: [PATCH] Update ivar to 1.4.2 (#5253)

Allows piping data from ivar trim into samtools sort.
---
 tools/ivar/ivar_trim.xml | 7 +------
 tools/ivar/macros.xml    | 2 +-
 2 files changed, 2 insertions(+), 7 deletions(-)

diff --git a/tools/ivar/ivar_trim.xml b/tools/ivar/ivar_trim.xml
index 0c7fed7e480..4110aa51054 100644
--- a/tools/ivar/ivar_trim.xml
+++ b/tools/ivar/ivar_trim.xml
@@ -40,12 +40,7 @@
         #end if
         -q $min_qual
         -s $window_width
-        ## since v1.4 ivar trim *almost* supports piping its output, but
-        ## unfortunately still writes *some* regular messages to stdout,
-        ## so we need to stick writing to an intermediate file for now and
-        ## want to unify the output stream
-        -p trimmed 1>&2 &&
-        samtools sort -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o trimmed.sorted.bam trimmed.bam
+        | samtools sort -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o trimmed.sorted.bam -
     ]]></command>
     <inputs>
         <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
diff --git a/tools/ivar/macros.xml b/tools/ivar/macros.xml
index 91c392b5e8d..0a15bfa08ab 100644
--- a/tools/ivar/macros.xml
+++ b/tools/ivar/macros.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-  <token name="@TOOL_VERSION@">1.4.0</token>
+  <token name="@TOOL_VERSION@">1.4.2</token>
   <token name="@PROFILE@">21.01</token>
   <xml name="requirements">
   <requirements>