Workflow: wf_amr_dna.cwl
Fetched 2023-01-04 02:00:38 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/ncbi/pipelines/85bd1acfc587e6a3ebce7ccf1ce93bf8b48e881c/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fam | File | ||
| fasta | File | ||
| query | File | ||
| ident_min | Float | ||
| num_threads | Integer (Optional) | ||
| query_gencode | Integer | ||
| parse_deflines | Boolean | ||
| complete_cover_min | Float |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| blastx |
blastx.cwl
(CommandLineTool)
|
||
| amr_report |
amr_report.cwl
(CommandLineTool)
|
||
| fasta_check |
fasta_check.cwl
(CommandLineTool)
|
||
| makeblastdb |
wf_makeblastdb.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| result | File | ||
| fasta_check_out | File |
Permalink:
https://w3id.org/cwl/view/git/85bd1acfc587e6a3ebce7ccf1ce93bf8b48e881c/amr_finder/wf_amr_dna.cwl
