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

Fetched 2023-01-04 16:39:36 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
lds2 File
taxid Integer
CDDdata Directory
CDDdata2 Directory
proteins File
taxon_db File
annotation File
genus_list Integer[]
thresholds File
naming_sqlite File
uniColl_cache Directory
blast_rules_db String
sequence_cache Directory
wp_assignments File
hmm_assignments File
naming_blast_db Directory
blast_hits_cache File (Optional)
blast_rules_db_dir Directory
defline_cleanup_rules File
identification_db_dir Directory
scatter_gather_nchunks String
Extract_Model_Proteins_prot_ids File
Good_AntiFam_filtered_proteins_gilist File

Steps

ID Runs Label Doc
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 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

Outputs

ID Type Label Doc
out_annotation File
Permalink: https://w3id.org/cwl/view/git/5463361069e263ad6455858e054c1337b1d9e752/bacterial_annot/wf_bacterial_annot_pass4.cwl