Bacterial Annotation, pass 2, blastp-based functional annotation (first pass) - Common Workflow Language Viewer

Workflow: Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)

Fetched 2024-11-23 01:05:21 GMT

Verified with cwltool version 3.1.20230201224320

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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	Doc
lds2	File	Extract ORF Proteins/lds2
taxid	Integer
blastdb	String[]	Input blastdb databases
plasmids	File	Prepare_Unannotated_Sequences/plasmids
proteins	File	Extract ORF Proteins/proteins
raw_seqs	File	Prepare_Unannotated_Sequences/sequences
taxon_db	File
annotation	File	Get ORFs/outseq
genus_list	Integer[]
prot_ids_A	File	Extract ORF Proteins/prot_ids
prot_ids_B1	File	Get off-frame ORFs/prot_ids
prot_ids_B2	File	AntiFam tainted proteins I/oseqids
unicoll_cache	Directory
blast_rules_db	String	parameter to store the literal 'blast_rules_db'
sequence_cache	Directory
blast_hits_cache	File (Optional)
identification_db_dir	Directory	Create identification BLASTdb
scatter_gather_nchunks	String

Steps

ID	Runs	Label	Doc
Map_Naming_Hits	bacterial_hit_mapping.cwl (CommandLineTool)	bacterial_hit_mapping
Remove_off_frame_ORFs	../progs/set_operation.cwl (CommandLineTool)	set_operation
Separate_Plasmid_ORFs	../progs/separate_plasmid_orfs.cwl (CommandLineTool)	separate_plasmid_orfs
Find_Naming_Protein_Hits_for_struct	../task_types/tt_blastp_wnode_naming.cwl (Workflow)	blastp_wnode_naming
Find_Struct_Protein_Hits_for_Plasmids	../task_types/tt_blastp_wnode_struct.cwl (Workflow)	blastp_wnode_struct

Outputs

ID	Type	Label	Doc
aligns	File	goes to protein_alignment/Seed Search Compartments/compartments

Permalink: https://w3id.org/cwl/view/git/5b498b4c4f17bb8f17e6886aa4c5661d7aba34fc/bacterial_annot/wf_bacterial_annot_pass2.cwl