Workflow: PGAP Pipeline
Fetched 2026-09-10 21:43:30 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fasta | File | ||
| taxid | Integer | ||
| hmm_hits | File | ||
| hmm_path | Directory | ||
| hmms_tab | File | ||
| model_path | File | ||
| gc_assm_name | String | ||
| uniColl_cache | Directory | ||
| rfam_stockholm | File | ||
| 16s_blastdb_dir | Directory | ||
| 23s_blastdb_dir | Directory | ||
| gene_master_ini | File | ||
| rfam_amendments | File | ||
| submit_block_template | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| genomic_source |
genomic_source/wf_genomic_source.cwl
(Workflow)
|
Create Genomic Collection for Bacterial Pipeline | |
| bacterial_annot |
bacterial_annot/wf_bacterial_annot.cwl
(Workflow)
|
Bacterial Annotation (two-pass) | |
| cache_entrez_gene |
cache_entrez_gene.cwl
(CommandLineTool)
|
Cache Entrez Gene | |
| bacterial_noncoding | Non-Coding Bacterial Genes | ||
| bacterial_prepare_unannotated |
bacterial_prepare_unannotated.cwl
(CommandLineTool)
|
Prepare Unannotated Sequences |
Note that this implementation skips asn validation steps. Please fix |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| aligns | File | ||
| annotations_5s | File | ||
| annotations_16s | File | ||
| annotations_23s | File | ||
| prok_entrez_gene_stuff | File |
Permalink:
https://w3id.org/cwl/view/git/21baa197e2c87a71e48794cef96d24c52518a99c/wf_pgap.cwl
