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Force full-length ivar consensus builds #5115

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Merged
wm75 merged 2 commits into from
Feb 10, 2023
Merged

Force full-length ivar consensus builds #5115

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88c9ddc
Force full-length ivar consensus builds
wm75 Feb 3, 2023
40d1f00
More fixes to the consensus tool
wm75 Feb 6, 2023
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4 changes: 2 additions & 2 deletions tools/ivar/ivar_consensus.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="ivar_consensus" name="ivar consensus" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
<tool id="ivar_consensus" name="ivar consensus" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
<description>Call consensus from aligned BAM file</description>
<macros>
<import>macros.xml</import>
Expand All @@ -9,7 +9,7 @@
#import re
#set $clean_name = re.sub('[^\w\-]', '_', str($input_bam.element_identifier))
ln -s '$input_bam' sorted.bam &&
samtools mpileup -A -d 0 -Q 0 sorted.bam | ivar consensus
samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus
-p consensus
-q $min_qual
-t $min_freq
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