- 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