Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)

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.

Inputs

ID	Type	Title
lds2	File
taxid	Integer
CDDdata	Directory
blastdb	String[]	Input blastdb databases
CDDdata2	Directory
proteins	File
taxon_db	File
annotation	File
genus_list	Integer[]
thresholds	File
naming_sqlite	File
uniColl_cache	Directory
blast_rules_db	String	parameter to store the literal 'blast_rules_db'
sequence_cache	Directory
wp_assignments	File
hmm_assignments	File
blast_hits_cache	File (Optional)
defline_cleanup_rules	File
identification_db_dir	Directory
scatter_gather_nchunks	String
Extract_Model_Proteins_prot_ids	File
Good_AntiFam_filtered_proteins_gilist	File

ID	Runs	Label
Add_Names_to_Proteins	../progs/add_prot_names_to_annot.cwl (CommandLineTool)	add_prot_names_to_annot
Bacterial_Annot_Filter	../progs/bact_annot_filter.cwl (CommandLineTool)	bact_annot_filter
Find_best_protein_hits	../progs/align_filter.cwl (CommandLineTool)	align_filter
Prepare_SPARCLBL_input	../progs/prepare_sparclbl_input.cwl (CommandLineTool)	prepare_sparclbl_input
Find_Naming_Protein_Hits	../task_types/tt_blastp_wnode_naming.cwl (Workflow)	blastp_wnode_naming
Assign_Clusters_to_Proteins	../progs/assign_cluster.cwl (CommandLineTool)	assign_cluster
Assign_Clusters_to_Proteins_sort	../progs/align_sort.cwl (CommandLineTool)	align_sort
Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl	../progs/sparclbl.cwl (CommandLineTool)	sparclbl
Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta	../progs/asn2fasta.cwl (CommandLineTool)	asn2fasta
Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences	../progs/gp_fetch_sequences.cwl (CommandLineTool)	gp_fetch_sequences

ID	Type	Label	Doc
out_annotation	File