Workflow: Indices builder from GBOL RDF (TTL)
Fetched 2023-01-09 00:22:17 GMT
Verified with cwltool version 3.1.20221201130942
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
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| memory | Integer (Optional) | maximum memory usage in megabytes |
maximum memory usage in megabytes |
| threads | Integer (Optional) | number of threads |
number of threads to use for computational processes |
| run_star | Boolean | Run STAR |
create STAR index for genome if true. (For genomes with exons) |
| inputFile | File | Input File |
Annotated genome in GBOL turtle file (.ttl) format |
| genomeSAindexNbases | Integer (Optional) | STAR parameter |
For small genomes, the parameter --genomeSAindexNbases must be scaled down. |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| STAR |
../RNAseq/star/star_index.cwl
(CommandLineTool)
|
STAR indexer |
Creates the Genome index for STAR spliced RNAseq aligner (single fasta) |
| bowtie2 |
../bowtie2/bowtie2_index.cwl
(CommandLineTool)
|
Bowtie2 indexer |
Creates the Genome index for bowtie2 (single fasta) |
| rdf2gtf |
../sapp/conversion_rdf2gtf.cwl
(CommandLineTool)
|
SAPP conversion RDF2GTF |
SAPP conversion tool utilizing the function RDF2GTF |
| kallisto |
../RNAseq/kallisto/kallisto_index.cwl
(CommandLineTool)
|
kallisto indexer |
Creates the index for pseudoalignment tool kallisto https://github.com/common-workflow-library/bio-cwl-tools/tree/release/Kallisto |
| rdf2fasta |
../sapp/conversion_rdf2fasta.cwl
(CommandLineTool)
|
SAPP conversion RDF2FASTA |
SAPP conversion tool utilizing the function RDF2FASTA |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gtf | File | GTF |
Genes in GTF format |
| STAR | Directory | STAR index |
Creates STAR index with genome fasta and GTF file |
| bowtie2 | Directory | bowtie2 index |
Creates bowtie2 index with genome fasta |
| kallisto | Directory | kallisto index |
Creates kallisto index with transcripts fasta file |
| proteins | File | Proteins |
Proteins fasta file |
| genomefasta | File | Genome fasta |
Genome fasta file |
| transcripts | File | Transcripts |
Transcripts fasta file |
https://w3id.org/cwl/view/git/cd0c19d51068c5407cd70b718a561d4662819d87/cwl/workflows/workflow_indexbuilder.cwl
