Create STAR mapper index module

This module allow to create a STAR mapper index with custom options. If this module is not declared in the workflow file, the default mapper index generator will be used if you want to use STAR as mapper.

  • Internal name: starindexgenerator
  • Available: Both local and distributed mode

  • Input ports:
    • genome: genome sequence file (format: genome_fasta)
    • genomedescription: genome description (automatically generated from genome sequence file)
    • annotation: genome annotation in GFF3 or GTF format (if required in parameters)

  • Output port:
    • output: genome mapper index

  • Mandatory parameters: none

  • Optional parameters:
  • Parameter Type Description Default value
    overhang integer Specifies the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database 100
    use.gtf.file boolean If true, the GFF3 annotation specified in the design file will be used by STAR to extract splice junctions. Using this option greatly improve the accuracy of the mapping. It is highly recommanded to use this option when feature annotation is available. None
    file.chr.start.end String Path to the file that contains the list of splice junctions coordinates None
    gtf.feature.exon String Feature type (3rd column in GFF file) to be used None
    gtf.tag.exon.parent.transcript String GFF attribute to be used as feature ID None
    features.file.format string The features file format. Currently only GFF/GFF3 and GTF format are supported. gff3 Integer See STAR documentation for more information None
    genome.chr.bin.nbits Integer See STAR documentation for more information None
    use.expression.step.parameters Boolean Use the genomictype and attributeid parameters values from an expression step to set the values of the gtf.feature.exon and gtf.tag.exon.parent.transcript parameters of this step False
    indexer.arguments String Additional indexer arguments Not set
  • Configuration example:
  • <!-- Create STAR index -->
    <step skip="false">