Indices builder from GBOL RDF (TTL)
Version 1

Workflow Type: Common Workflow Language

Workflow to build different indices for different tools from a genome and transcriptome.

This workflow expects an (annotated) genome in GBOL ttl format.


  • SAPP: rdf2gtf (genome fasta)
  • SAPP: rdf2fasta (transcripts fasta)
  • STAR index (Optional for Eukaryotic origin)
  • bowtie2 index
  • kallisto index

Click and drag the diagram to pan, double click or use the controls to zoom.


ID Name Description Type
threads number of threads number of threads to use for computational processes
  • int?
memory maximum memory usage in megabytes maximum memory usage in megabytes
  • int?
inputFile turtle file Annotated genome in GBOL turtle file (.ttl) format
  • File
run_star Run STAR create STAR index for genome if true. (For genomes with exons)
  • boolean
genomeSAindexNbases STAR parameter For small genomes, the parameter --genomeSAindexNbases must be scaled down.
  • int?


ID Name Description
rdf2gtf RDF to GTF Convert input RDF (turtle) file to GTF file
rdf2fasta RDF to Fasta Convert input RDF (turtle) file to Genome fasta file.
STAR STAR index Creates STAR index with genome fasta and GTF file
bowtie2 bowtie2 index Creates bowtie2 index with genome fasta
kallisto kallisto index Creates kallisto index with transcripts fasta file


ID Name Description Type
STAR STAR STAR index folder
  • Directory
bowtie2 bowtie2 bowtie2 index folder
  • Directory
kallisto kallisto kallisto index folder
  • Directory
genomefasta Genome fasta Genome fasta file
  • File
gtf GTF Genes in GTF format
  • File
transcripts Transcripts Transcripts fasta file
  • File
proteins Proteins Proteins fasta file
  • File

Version History

Version 1 (earliest) Created 23rd Nov 2020 at 16:22 by Bart Nijsse

Added/updated 1 files

Open master f8d3db7
help Creators and Submitter
Discussion Channel

Views: 1618   Downloads: 101

Created: 23rd Nov 2020 at 16:22

help Tags
help Attributions


Total size: 4.34 KB
Powered by
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH