Indices builder from GBOL RDF (TTL)
Version 1

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Workflow Type: Common Workflow Language

Work-in-progress

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

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

Steps:

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SEEK ID: https://workflowhub.eu/workflows/75?version=1

Inputs

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