bacterial_orthology - Common Workflow Language Viewer

Workflow: bacterial_orthology

Fetched 2025-08-30 18:53:26 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/8af4e2aabf43d5e3c7162efae4ad4649df5601e2/LICENSE.md

Note that the tools invoked by the workflow may have separate licenses.

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	../progs/protein_extract.cwl (Workflow)	protein_extract
extract_protein_references_for_orthology	../progs/protein_extract.cwl (Workflow)	protein_extract
get_assemblies_for_orthologs_gencoll_asn	../task_types/tt_gcaccess_from_list.cwl (Workflow)	gcaccess_from_list
create_orthologous_prokaryotic_protein_blastdb	../progs/gp_makeblastdb.cwl (Workflow)	gp_makeblastdb
blastp_current_prokaryotic_proteins_vs_orthologs	../task_types/tt_blastp_wnode_naming.cwl (Workflow)	blastp_wnode_naming

Outputs

ID	Type	Label	Doc
output	File

Permalink: https://w3id.org/cwl/view/git/8af4e2aabf43d5e3c7162efae4ad4649df5601e2/bacterial_orthology/wf_bacterial_orthology.cwl