Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)

Workflow: Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)

Fetched 2025-04-23 10:25:24 GMT

Verified with cwltool version 3.1.20230201224320

This workflow is Open Source and may be reused according to the terms of: https://raw.githubusercontent.com/ncbi/pgap/master/LICENSE.md

Note that the tools invoked by the workflow may have separate licenses.

ID	Type	Title	Doc
go	Boolean[]
inseq	File
asn_cache	Directory
nogenbank	Boolean
thresholds	File
trna_annots	File
ncrna_annots	File
genemark_path	String
naming_sqlite	File
uniColl_cache	Directory
selenoproteins	Directory
selenoproteins_db	String
Execute_CRISPRs_annots	File
Generate_16S_rRNA_Annotation_annotation	File
Generate_23S_rRNA_Annotation_annotation	File
Post_process_CMsearch_annotations_annots_5S	File

ID	Runs	Label
Run_GeneMark_Training	../progs/genemark_training.cwl (CommandLineTool)	genemark_training
Run_GeneMark_Training_post	../progs/genemark_post.cwl (CommandLineTool)	genemark_post
Resolve_Annotation_Conflicts	../progs/bacterial_resolve_conflicts.cwl (CommandLineTool)	bacterial_resolve_conflicts

ID	Type	Label	Doc
models1	File
annotation	File
out_hmm_params	File (Optional)
protein_aligns	File