Update ivar to 1.4.2 (galaxyproject#5253)

Allows piping data from ivar trim into samtools sort.
bebatut · Apr 19, 2023 · 51d6565 · 51d6565
1 parent ce8ee43
commit 51d6565
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diff --git 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
@@ -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>