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 10:25:26 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/test/LICENSE.md

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

ID	Type	Title	Doc
go	Boolean[]
inseq	File
hmm_path	Directory
hmms_tab	File
asn_cache	Directory
nogenbank	Boolean
annotation	File
uniColl_cache	Directory
scatter_gather_nchunks	String

ID	Runs	Label
Get_ORFs	../progs/gp_getorf.cwl (CommandLineTool)	gp_getorf
Filter_ORFs	../progs/bact_filter_orfs.cwl (CommandLineTool)	bact_filter_orfs
Map_HMM_Hits	bacterial_hit_mapping.cwl (CommandLineTool)	bacterial_hit_mapping
Search_All_HMMs	../task_types/tt_hmmsearch_wnode.cwl (Workflow)
Get_off_frame_ORFs	get_off_frame_orfs.cwl (CommandLineTool)	Get off-frame ORFs
Extract_All_ORF_Proteins	../progs/protein_extract.cwl (Workflow)	protein_extract
Extract_Accepted_ORF_Proteins	../progs/protein_extract.cwl (Workflow)	protein_extract

ID	Type	Label	Doc
lds2	File
aligns	File
seqids	File
outseqs	File
hmm_hits	File
prot_ids	File
proteins	File