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Anonymous committed 27c25ed

several modifications made to the xml bowtie

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  • Parent commits 43c2dbf

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tools/sr_mapping/bowtie2_wrapper.xml

         bowtie2_wrapper.py
         
         ## Change this to accommodate the number of threads you have available.
-        --num-threads="4"
+        --num-threads="32"
 
         ## Outputs.
         --output=$output
                 <param format="fastqsanger" name="input2" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
                 <!-- TODO: paired-end specific parameters. -->
                 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
-                <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
+                <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
             </when>
         </conditional>
         <param name="unalignedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (uses --un for single-end and  --un-conc for paired-ends)" />