Workflow Type: Common Workflow Language
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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
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
ID | Name | Description | Type |
---|---|---|---|
threads | number of threads | number of threads to use for computational processes |
|
memory | maximum memory usage in megabytes | maximum memory usage in megabytes |
|
inputFile | turtle file | Annotated genome in GBOL turtle file (.ttl) format |
|
run_star | Run STAR | create STAR index for genome if true. (For genomes with exons) |
|
genomeSAindexNbases | STAR parameter | For small genomes, the parameter --genomeSAindexNbases must be scaled down. |
|
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 |
|
bowtie2 | bowtie2 | bowtie2 index folder |
|
kallisto | kallisto | kallisto index folder |
|
genomefasta | Genome fasta | Genome fasta file |
|
gtf | GTF | Genes in GTF format |
|
transcripts | Transcripts | Transcripts fasta file |
|
proteins | Proteins | Proteins fasta file |
|
Version History
Version 1 (earliest) Created 23rd Nov 2020 at 16:22 by Bart Nijsse
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Views: 2458 Downloads: 291
Created: 23rd Nov 2020 at 16:22
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