Workflow: bacterial_orthology

Fetched 2024-05-30 10:23:34 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
input File
taxid Integer
blastdb String[]
gc_cache File
taxon_db File
asn_cache Directory[]
genus_list Integer[]
gencoll_asn File
naming_sqlite File
gc_id_list_orth File
blast_hits_cache File (Optional)
scatter_gather_nchunks String

Steps

ID Runs Label Doc
cat_aligns
../progs/cat.cwl (CommandLineTool)

concatenates input File[] to output File

prepare_annotation_input
../progs/asn_translator.cwl (CommandLineTool)
asn_translator
find_prokarotic_orthologs
../progs/find_orthologs.cwl (CommandLineTool)
find_orthologs
propagate_symbols_to_genes
../progs/propagate_symbols_to_genes.cwl (CommandLineTool)
propagate_symbols_to_genes
get_ortholog_nucleotide_ids
../progs/gc_get_molecules.cwl (CommandLineTool)
gc_get_molecules
extract_ortholog_nucleotide_asn
../progs/gp_fetch_sequences.cwl (CommandLineTool)
gp_fetch_sequences
extract_protein_targets_for_orthology protein_extract
extract_protein_references_for_orthology protein_extract
get_assemblies_for_orthologs_gencoll_asn gcaccess_from_list
create_orthologous_prokaryotic_protein_blastdb gp_makeblastdb
blastp_current_prokaryotic_proteins_vs_orthologs blastp_wnode_naming

Outputs

ID Type Label Doc
output File
Permalink: https://w3id.org/cwl/view/git/c7c674b873b9925b28ffbd602974eec4bfe78cf9/bacterial_orthology/wf_bacterial_orthology.cwl