Workflow: PGAP Pipeline, simple user input, GP-24057
Fetched 2026-09-16 09:42:30 GMT
Verified with cwltool version 3.1.20230201224320
PGAP pipeline for external usage, powered via Docker 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-gpipe/pgap/c08fd46e8f715b9b5aa487466705863e4b1829df/GeneMarkS_Software_License.txt
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| tech | String (Optional) | ||
| fasta | File | ||
| taxid | Integer | ||
| CDDdata | Directory | ||
| CDDdata2 | Directory | ||
| hmm_path | Directory | ||
| hmms_tab | File | ||
| taxon_db | File | ||
| wp_hashes | File | ||
| AntiFamLib | Directory | ||
| thresholds | File | ||
| asn2pas_xsl | File | ||
| completeness | String (Optional) | ||
| gc_assm_name | String | ||
| 5s_model_path | File | ||
| genemark_path | Directory | ||
| naming_sqlite | File | ||
| uniColl_cache | Directory | ||
| univ_prot_xml | File | ||
| blast_rules_db | String | ||
| rfam_stockholm | File | ||
| selenoproteins | Directory | ||
| 16s_blastdb_dir | Directory | ||
| 23s_blastdb_dir | Directory | ||
| gene_master_ini | File | ||
| molinfo_wgs_asn | File | ||
| naming_blast_db | Directory | ||
| naming_hmms_tab | File | ||
| rfam_amendments | File | ||
| rfam_model_path | File | ||
| val_res_den_xml | File | ||
| blast_rules_db_dir | Directory | ||
| molinfo_complete_asn | File | ||
| naming_hmms_combined | Directory | ||
| defline_cleanup_rules | File | ||
| submit_block_template | File | ||
| submit_block_template_static | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| standard_pgap |
wf_pgap.cwl
(Workflow)
|
PGAP Pipeline |
PGAP pipeline for external usage, powered via Docker 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/c08fd46e8f715b9b5aa487466705863e4b1829df/wf_pgap_simple2.cwl
