Workflow: wf_amr_prot.cwl
Fetched 2024-04-26 07:12:34 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/master/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| cpu | Integer (Optional) | ||
| fam | File | ||
| gff | File (Optional) | ||
| fasta | File | ||
| hmmdb | File | ||
| query | File | ||
| num_threads | Integer (Optional) | ||
| parse_deflines | Boolean |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| blastp |
blastp.cwl
(CommandLineTool)
|
||
| gff_check |
gff_check.cwl
(CommandLineTool)
|
||
| hmmsearch |
hmmsearch.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 | ||
| gff_check_out | File | ||
| fasta_check_out | File |
Permalink:
https://w3id.org/cwl/view/git/7a5fae087e42ec7d2bfdf3f88ba2ea1e8fdc9ddf/amr_finder/wf_amr_prot.cwl
