# HG changeset patch
# User iuc
# Date 1531573619 14400
# Node ID 0b1c04a9018242d8385720af67da441d657fd914
# Parent  6ab42baa56e913fe6989b768757a2604dfba50cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit dac38d1735c11fe614d0a986a796e33eb7f4a469

diff -r 6ab42baa56e9 -r 0b1c04a90182 hisat2.xml
--- a/hisat2.xml	Wed May 30 12:02:20 2018 -0400
+++ b/hisat2.xml	Sat Jul 14 09:06:59 2018 -0400
@@ -1,11 +1,11 @@
-<tool id="hisat2" name="HISAT2" version="2.1.0" profile="17.01">
+<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy1" profile="17.01">
     <description>A fast and sensitive alignment program</description>
     <macros>
         <import>hisat2_macros.xml</import>
     </macros>
     <requirements>
         <requirement type="package" version="2.1.0">hisat2</requirement>
-        <requirement type="package" version="1.4">samtools</requirement>
+        <requirement type="package" version="1.8">samtools</requirement>
     </requirements>
     <stdio>
         <regex level="fatal" match="hisat2-align exited with value 1" source="both" />
@@ -14,9 +14,6 @@
     </stdio>
     <version_command>hisat2 --version</version_command>
     <command><![CDATA[
-## Use pipefail if available to quit with first non-zero exit code
-set -o | grep -q pipefail && set -o pipefail;
-
 ## Prepare HISAT2 index
 
 #if $reference_genome.source == "history":
@@ -293,8 +290,16 @@
 #end if
 
 ## Convert SAM output to sorted BAM
+## using the two pipe stages has the following effect
+## - hisat2 and sort run in parallel, during this time sort produces
+##   presorted temporary files but does not produce output (hence 
+##   view does not run)
+## - once hisat is finished sort will start to merge the temporary 
+##   files (which should be fast also on a single thread) gives the 
+##   sorted output to view which only compresses the files (now 
+##   using full parallelism again)
 
-| samtools sort - -@ \${GALAXY_SLOTS:-1} -l 6 -o '${output_alignments}'
+| samtools sort -l 0 -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}'
 
 ## Rename any output fastq files