Workflow: Genome conversion and annotation
Fetched 2023-01-03 19:48:29 GMT
Verified with cwltool version 3.1.20221201130942
Workflow for genome annotation from EMBL format
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| embl | File | EMBL input file |
Genome sequence in EMBL format |
| codon | Integer | Codon table |
Codon table used for gene prediction |
| threads | Integer (Optional) | number of threads |
number of threads to use for computational processes |
| identifier | String | Sample name |
Identifier of the sample being converted |
| destination | String (Optional) | Output Destination |
Optional Output destination used for cwl-prov reporting. |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gzip |
../bash/compress.cwl
(CommandLineTool)
|
compress any file with gzip | |
| prodigal |
../sapp/prodigal.cwl
(CommandLineTool)
|
Gene prediction |
Runs microbial gene prediction on GBOL RDF file |
| kofamscan |
../sapp/kofamscan.cwl
(CommandLineTool)
|
Gene prediction |
Runs KEGG KO annotation on protein sequences using SAPP. Requires a kofamscan conda environment. |
| conversion |
../sapp/conversion.cwl
(CommandLineTool)
|
Genome conversion |
Runs Genome conversion tool from SAPP |
| interproscan |
../sapp/interproscan.cwl
(CommandLineTool)
|
InterProScan annotation |
Runs Genome annotation with InterProScan using an RDF genome file according to the GBOL ontology |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output | File |
Permalink:
https://w3id.org/cwl/view/git/b9097b82e6ab6f2c9496013ce4dd6877092956a0/cwl/workflows/workflow_sapp_microbes.cwl
