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pjbriggs/Galactic-Engineer-GALAXY_SLOTS-trimmomatic-fragment.xml

Created April 22, 2015 12:01
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Galactic Engineer/GALAXY_SLOTS: trimmomatic.xml fragment
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Galactic-Engineer-GALAXY_SLOTS-trimmomatic-fragment.xml
...
<command interpreter="bash">trimmomatic.sh
-mx8G
-jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar
#if $paired_end.is_paired_end
PE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_r1_in $paired_end.fastq_r2_in $fastq_out_r1_paired $fastq_out_r1_unpaired $fastq_out_r2_paired $fastq_out_r2_unpaired
#else
SE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_in $fastq_out
#end if
...
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