Workflow: PGAP Pipeline, simple user input
Fetched 2023-01-10 14:30:23 GMT
Verified with cwltool version 3.1.20221201130942
PGAP pipeline for external usage, powered via containers, simple user input: (FASTA + yaml only, no template)
- 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/pgap/a79cec2331b3e17e382e8e5040405e8dd750c639/LICENSE.md
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| tech | String (Optional) | ||
| fasta | File | ||
| taxid | Integer | ||
| completeness | String (Optional) | ||
| gc_assm_name | String | ||
| report_usage | Boolean | ||
| blast_rules_db | String | ||
| molinfo_wgs_asn | File | ||
| supplemental_data | Directory | ||
| molinfo_complete_asn | File | ||
| submit_block_template | File | ||
| submit_block_template_static | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| standard_pgap |
wf_common.cwl
(Workflow)
|
PGAP Pipeline |
PGAP pipeline for external usage, powered via containers |
| prepare_input_template |
prepare_user_input.cwl
(CommandLineTool)
|
Prepare user input |
Prepare user input for NCBI-PGAP pipeline |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gbk | File | ||
| gff | File | ||
| gbent | File | ||
| protein_fasta | File (Optional) | ||
| nucleotide_fasta | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/a79cec2331b3e17e382e8e5040405e8dd750c639/wf_pgap_simple.cwl
