Workflow: star-index.cwl
Fetched 2023-04-15 10:06:10 GMT
Verified with cwltool version 3.1.20230201224320
Generates indices for STAR v2.5.3a (03/17/2017).
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fasta | File [FASTA] | FASTA input file |
Reference genome input FASTA file |
| genome | String | Genome |
Used by BioWardrobe to set genome |
| threads | Integer (Optional) | Number of threads to run tools |
Number of threads for those steps that support multithreading |
| annotation_gtf | File [GTF] | GTF input file |
Annotation input file |
| annotation_tab | File [TSV] | Annotation file |
Tab-separated annotation file |
| genome_sa_sparse_d | Integer (Optional) | Use 2 to decrease needed RAM for STAR |
int>0: suffux array sparsity, i.e. distance between indices: use bigger numbers to decrease needed RAM at the cost of mapping speed reduction |
| effective_genome_size | String | Effective genome size |
MACS2 effective genome size: hs, mm, ce, dm or number, for example 2.7e9 |
| limit_genome_generate_ram | Long (Optional) |
31000000000 int>0: maximum available RAM (bytes) for genome generation |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| star_generate_indices |
../tools/star-genomegenerate.cwl
(CommandLineTool)
|
Runs STAR genomeGenerated. Returns directory with index |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| annotation | File [TSV] | Annotation file |
Tab-separated annotation file |
| genome_size | String | Effective genome size |
MACS2 effective genome size: hs, mm, ce, dm or number, for example 2.7e9 |
| chrom_length | File [Textual format] | Chromosome length file |
Chromosome length file |
| star_indices | Directory | STAR indices folder |
Folder which includes all STAR generated indices files |
Permalink:
https://w3id.org/cwl/view/git/cf107bc24a37883ef01b959fd89c19456aaecc02/workflows/star-index.cwl
