CWL Workflow: bacterial_kmer

Workflow: bacterial_kmer

Fetched 2023-01-05 05:01:26 GMT

Verified with cwltool version 3.1.20221201130942

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This workflow is Open Source and may be reused according to the terms of: https://raw.githubusercontent.com/ncbi/pgap/2d54b11cc9891c9aa52515fe4f8cd9cba12c6629/LICENSE.md

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

Inputs

ID	Type	Title	Doc
gc_cache	File
taxon_db	File
asn_cache	Directory
tax_synon	File
ANI_cutoff	File
gencoll_asn	File
gc_seq_cache	Directory
ref_assembly_id	Integer
gcextract2_sqlite	File
kmer_cache_sqlite	File
ref_assembly_taxid	Integer
ani_report_transform	File
kmer_reference_assemblies	File
Extract_Kmers_From_Input___entry	File

Steps

ID	Runs	Label	Doc
List_sqlite	../progs/list_kmer_sqlite.cwl (CommandLineTool)	list_kmer_sqlite.cwl	Produces the list of all keys in sqlite database
Compare_Kmer	../task_types/tt_kmer_ref_compare_wnode.cwl (Workflow)	kmer_ref_compare_wnode
Identify_Top_N	../task_types/tt_kmer_top_n.cwl (Workflow)
Build_Kmer_Tree	../task_types/tt_kmer_build_tree.cwl (Workflow)	kmer_build_tree
Identify_Top_N_ANI	../task_types/tt_ani_top_n.cwl (Workflow)	ani_top_n
Combine_kmer_sqlite	../progs/combine_kmer_sqlite.cwl (CommandLineTool)	combine_kmer_sqlite.cwl	Combine together reference kmer store and newly created kmer store for a new assembly
Extract_Top_Assemblies	../task_types/tt_kmer_top_n_extract.cwl (Workflow)	kmer_top_n_extract
Compare_Kmer__Pairwise_	../task_types/tt_kmer_compare_wnode.cwl (Workflow)	tt_kmer_compare_wnode	Pairwise comparison
Assembly_Assembly_BLASTn	../task_types/tt_assm_assm_blastn_wnode.cwl (Workflow)	assm_assm_blastn_wnode
Extract_Kmers_From_Input	../task_types/tt_kmer_seq_entry_extract_wnode.cwl (Workflow)	kmer_seq_entry_extract_wnode
Extract_Input_GenColl_IDs	../progs/gc_extract_ids.cwl (CommandLineTool)	gc_extract_ids
Convert_kmer_files_to_sqlite	../progs/kmer_files2sqlite.cwl (CommandLineTool)	kmer_files2sqlite.cwl	Convert input .kmer.gz (kmer_file) and .xml (kmer_metadata_file) into new sqlite database Takes a directory input
Identify_Top_N_ANI_transform	../progs/xsltproc.cwl (CommandLineTool)	xsltproc
Get_Top_Assemblies_GenColl_ASN	../task_types/tt_gcaccess_from_list.cwl (Workflow)	gcaccess_from_list
Compare_Kmer_Pairwise_prepare_input	../progs/cat.cwl (CommandLineTool)		concatenates input File[] to output File

Outputs

ID	Type	Label	Doc
Identify_Top_N_ANI_top	File
Identify_Top_N_ANI_annot	File
Identify_Top_N_ANI_top_txt	File
Extract_Top_Assemblies___tax_report	File

Permalink: https://w3id.org/cwl/view/git/2d54b11cc9891c9aa52515fe4f8cd9cba12c6629/bacterial_kmer/wf_bacterial_kmer.cwl