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:
SAPP: rdf2gtf (genome fasta)
SAPP: rdf2fasta (transcripts fasta)
STAR index (Optional for Eukaryotic origin)
bowtie2 index
kallisto index
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? |
Steps
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 |
Outputs
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 |