Workflow: bacterial_kmer

Fetched 2023-01-09 23:53:04 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs gc_seq_cache gc_seq_cache Identify_Top_N_ANI ani_top_n gc_seq_cache->Identify_Top_N_ANI asn_cache Assembly_Assembly_BLASTn assm_assm_blastn_wnode gc_seq_cache->Assembly_Assembly_BLASTn gc_seq_cache asn_cache asn_cache asn_cache->Identify_Top_N_ANI asn_cache asn_cache->Assembly_Assembly_BLASTn asn_cache Extract_Kmers_From_Input kmer_seq_entry_extract_wnode asn_cache->Extract_Kmers_From_Input asn_cache Extract_Kmers_From_Input___entry Extract_Kmers_From_Input___entry Extract_Kmers_From_Input___entry->Extract_Kmers_From_Input entry gcextract2_sqlite gcextract2_sqlite Extract_Top_Assemblies kmer_top_n_extract gcextract2_sqlite->Extract_Top_Assemblies gcextract2_sqlite gcextract2_sqlite->Identify_Top_N_ANI gcextract2_sqlite taxon_db taxon_db taxon_db->Extract_Top_Assemblies taxon_db taxon_db->Identify_Top_N_ANI taxon_db kmer_cache_sqlite kmer_cache_sqlite Combine_kmer_sqlite combine_kmer_sqlite.cwl kmer_cache_sqlite->Combine_kmer_sqlite kmer_cache_sqlite gencoll_asn gencoll_asn gencoll_asn->Identify_Top_N_ANI gencoll_asn gencoll_asn->Assembly_Assembly_BLASTn gencoll_asn Extract_Input_GenColl_IDs gc_extract_ids gencoll_asn->Extract_Input_GenColl_IDs input ANI_cutoff ANI_cutoff ANI_cutoff->Identify_Top_N_ANI ANI_cutoff gc_cache gc_cache gc_cache->Assembly_Assembly_BLASTn gc_cache Get_Top_Assemblies_GenColl_ASN gcaccess_from_list gc_cache->Get_Top_Assemblies_GenColl_ASN gc_cache ref_assembly_taxid ref_assembly_taxid ref_assembly_taxid->Extract_Top_Assemblies ref_assembly_taxid ref_assembly_taxid->Identify_Top_N_ANI ref_assembly_taxid kmer_reference_assemblies kmer_reference_assemblies kmer_reference_assemblies->Extract_Kmers_From_Input kmer_file_list Compare_Kmer kmer_ref_compare_wnode kmer_reference_assemblies->Compare_Kmer ref_kmer_list ref_assembly_id ref_assembly_id ref_assembly_id->Extract_Top_Assemblies ref_assembly_id ref_assembly_id->Identify_Top_N_ANI ref_assembly_id tax_synon tax_synon tax_synon->Identify_Top_N_ANI tax_synon ani_report_transform ani_report_transform Identify_Top_N_ANI_transform xsltproc ani_report_transform->Identify_Top_N_ANI_transform xslt Extract_Top_Assemblies___tax_report Extract_Top_Assemblies___tax_report Identify_Top_N_ANI_annot Identify_Top_N_ANI_annot Identify_Top_N_ANI_top Identify_Top_N_ANI_top Identify_Top_N_ANI_top_txt Identify_Top_N_ANI_top_txt errors errors Extract_Top_Assemblies->Extract_Top_Assemblies___tax_report Extract_Top_Assemblies->Assembly_Assembly_BLASTn subjects_gc_id_list Extract_Top_Assemblies->Get_Top_Assemblies_GenColl_ASN gc_id_list Build_Kmer_Tree kmer_build_tree List_sqlite list_kmer_sqlite.cwl Compare_Kmer_Pairwise_prepare_input Compare_Kmer_Pairwise_prepare_input List_sqlite->Compare_Kmer_Pairwise_prepare_input input List_sqlite->Compare_Kmer kmer_list Identify_Top_N_ANI->Identify_Top_N_ANI_annot Identify_Top_N_ANI->Identify_Top_N_ANI_top Evaluate_ANI_report xml_evaluate Identify_Top_N_ANI->Evaluate_ANI_report input Identify_Top_N_ANI->Identify_Top_N_ANI_transform xml Evaluate_ANI_report->errors Assembly_Assembly_BLASTn->Identify_Top_N_ANI blast_align Convert_kmer_files_to_sqlite kmer_files2sqlite.cwl Extract_Kmers_From_Input->Convert_kmer_files_to_sqlite kmer_dir Combine_kmer_sqlite->Compare_Kmer kmer_cache_sqlite Compare_Kmer__Pairwise_ tt_kmer_compare_wnode Combine_kmer_sqlite->Compare_Kmer__Pairwise_ kmer_cache_sqlite Identify_Top_N Identify_Top_N Combine_kmer_sqlite->Identify_Top_N kmer_cache_sqlite Compare_Kmer_Pairwise_prepare_input->Compare_Kmer__Pairwise_ kmer_list Identify_Top_N_ANI_transform->Identify_Top_N_ANI_top_txt Compare_Kmer->Identify_Top_N distances Compare_Kmer__Pairwise_->Build_Kmer_Tree distances Identify_Top_N->Extract_Top_Assemblies top_distances Identify_Top_N->Compare_Kmer_Pairwise_prepare_input input Get_Top_Assemblies_GenColl_ASN->Identify_Top_N_ANI ref_gencoll_asn Get_Top_Assemblies_GenColl_ASN->Assembly_Assembly_BLASTn ref_gencoll_asn Extract_Input_GenColl_IDs->Assembly_Assembly_BLASTn queries_gc_id_list Convert_kmer_files_to_sqlite->List_sqlite kmer_cache_sqlite Convert_kmer_files_to_sqlite->Combine_kmer_sqlite kmer_cache_sqlite
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

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 kmer_ref_compare_wnode
Identify_Top_N
Build_Kmer_Tree kmer_build_tree
Identify_Top_N_ANI 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

Evaluate_ANI_report
../progs/xml_evaluate.cwl (CommandLineTool)
xml_evaluate
Extract_Top_Assemblies kmer_top_n_extract
Compare_Kmer__Pairwise_ tt_kmer_compare_wnode

Pairwise comparison

Assembly_Assembly_BLASTn assm_assm_blastn_wnode
Extract_Kmers_From_Input 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 gcaccess_from_list
Compare_Kmer_Pairwise_prepare_input
../progs/cat.cwl (CommandLineTool)

concatenates input File[] to output File

Outputs

ID Type Label Doc
errors File (Optional)
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
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