Workflow: PGAP Pipeline, simple user input, PGAPX-134
Fetched 2025-10-26 20:59:57 GMT
Verified with cwltool version 3.1.20230201224320
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/4e7b8f243f5356653edd286eab24f419f39da189/LICENSE.md
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fasta | File | ||
| submol | File | ||
| uuid_in | File (Optional) | ||
| make_uuid | Boolean (Optional) | ||
| os_version | String (Optional) | ||
| no_internet | Boolean (Optional) | ||
| report_usage | Boolean | ||
| ignore_all_errors | Boolean (Optional) | ||
| supplemental_data | Directory | ||
| blast_hits_cache_data | Directory (Optional) | ||
| xpath_fail_final_asndisc | String (Optional) | ||
| xpath_fail_initial_asndisc | String (Optional) | ||
| xpath_fail_final_asnvalidate | String (Optional) | ||
| xpath_fail_initial_asnvalidate | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastaval |
progs/fastaval.cwl
(CommandLineTool)
|
fastaval | |
| passdata |
9e64e11fb08750746817cd0eb8ff75f3
(ExpressionTool)
|
||
| standard_pgap |
wf_common.cwl
(Workflow)
|
PGAP Pipeline |
PGAP pipeline for external usage, powered via containers |
| prepare_input_template |
prepare_user_input2.cwl
(Workflow)
|
Prepare user input |
Prepare user input for NCBI-PGAP pipeline |
| Generate_Annotation_Reports_gff_enhanced |
progs/produce_enhanced_gff.cwl
(CommandLineTool)
|
Produce Roary input |
Produce Prokka and Roary ready GFF enhancement = GFF + nuc FASTA |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gbk | File | ||
| gff | File | ||
| sqn | File | ||
| calls | File | ||
| checkm_raw | File | ||
| input_fasta | File | ||
| gff_enhanced | File | ||
| input_submol | File | ||
| protein_fasta | File (Optional) | ||
| fastaval_errors | File | ||
| nucleotide_fasta | File (Optional) | ||
| cds_protein_fasta | File (Optional) | ||
| cds_nucleotide_fasta | File (Optional) | ||
| final_asnval_error_diag | File (Optional) | ||
| final_asndisc_error_diag | File (Optional) | ||
| initial_asnval_error_diag | File (Optional) | ||
| initial_asndisc_error_diag | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/4e7b8f243f5356653edd286eab24f419f39da189/pgap.cwl
