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

Fetched 2023-01-14 17:40:31 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
lds2 File Extract ORF Proteins/lds2
taxid Integer
proteins File Extract ORF Proteins/proteins
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 Name of blast_rules_db
sequence_cache Directory
blast_hits_cache File (Optional)
blast_rules_db_dir Directory Get BLAST Rules db const
identification_db_dir Directory Create identification BLASTdb
scatter_gather_nchunks String

Steps

ID Runs Label Doc
Map_Naming_Hits
bacterial_hit_mapping.cwl (CommandLineTool)
Map HMM Hits
Remove_off_frame_ORFs
../progs/set_operation.cwl (CommandLineTool)
set_operation
Find_Naming_Protein_Hits_I blastp_wnode_naming

Outputs

ID Type Label Doc
aligns File goes to protein_alignment/Seed Search Compartments/compartments
Permalink: https://w3id.org/cwl/view/git/1a6b9e5dea09caa0debbaff30ca39005dfa5e4d4/bacterial_annot/wf_bacterial_annot_pass2.cwl