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STAR: Add two pass mode #1726

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merged 5 commits into from
Feb 26, 2018
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STAR: Add two pass mode #1726

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9016aa6
Add two pass mode
TorHou Feb 16, 2018
26e4eac
Fix whitespace.
TorHou Feb 16, 2018
8895f54
Avoid parameter conflict
TorHou Feb 16, 2018
b47c1a2
Closing if
TorHou Feb 16, 2018
e4267f8
Bump version
TorHou Feb 16, 2018
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23 changes: 17 additions & 6 deletions tools/rgrnastar/rg_rnaStar.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="rna_star" name="RNA STAR" version="2.5.2b-1" profile="17.01">
<tool id="rna_star" name="RNA STAR" version="2.5.2b-2" profile="17.01">
<description>Gapped-read mapper for RNA-seq data</description>
<macros>
<import>macros.xml</import>
Expand Down Expand Up @@ -120,8 +120,9 @@
--alignSJDBoverhangMin 10
--alignMatesGapMax 200000
--alignIntronMax 200000
--twopassMode Basic
--twopass1readsN -1

## --twopass1readsN 100000000
## --chimSegmentReadGapMax 3 ## not an option in STAR 2.4.0
## --alignSJstitchMismatchNmax 5 -1 5 5 ## not an option in STAR 2.4.0

Expand Down Expand Up @@ -150,6 +151,12 @@
--alignTranscriptsPerReadNmax "$params.align.alignTranscriptsPerReadNmax"
--alignEndsType $params.align.alignEndsType

## Two pass mode
--twopassMode "$params.twopass.twopassMode"
#if str( $params.twopass.twopassMode ) == "Basic":
--twopass1readsN "$params.twopass.twopass1readsN"
#end if

## Chimeric alignment parameter options
#if str( $params.chim.chim_select ) == "yes":
--chimSegmentMin "$params.chim.chimSegmentMin"
Expand Down Expand Up @@ -325,11 +332,16 @@
<param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/>
</section>

<section name="twopass" title="Two pass mode" expanded="False">
<param argument="--twopassMode" type="boolean" truevalue="Basic" falsevalue="None" checked="false" label="Use two pass mode to better map reads to unknown splice junctions"/>
<param argument="--twopass1readsN" type="integer" min="-1" value="-1" label="Number of reads to map in the first pass (-1: all)"/>
</section>

<section name="limits" title="Limits" expanded="False">
<param argument="--limitBAMsortRAM" type="integer" min="0" value="0" label="Maximum available RAM (in bytes) for sorting" help="If 0, this will be set to the genome index size. This is typically only changed in cases where an error is produced." />
<param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
<param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
<param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
<param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
<param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
<param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
</section>

<conditional name="chim">
Expand Down Expand Up @@ -571,7 +583,6 @@ The All option includes the Standard attributes, plus the following four::
STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running
STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::

--twopassMode Basic # not an option in STAR 2.4.0
--chimSegmentReadGapMax 3 # not an option in STAR 2.4.0
--alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0

Expand Down