Workflow: taxcheck.cwl

Fetched 2023-01-10 01:26:09 GMT

Perform taxonomic identification tasks on an input genome

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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs no_internet no_internet prepare_input_template Prepare user input no_internet->prepare_input_template no_internet report_usage report_usage ping_stop pinger report_usage->ping_stop report_usage ping_start pinger report_usage->ping_start report_usage supplemental_data supplemental_data passdata Split input directory into subpath flows for top level user workflow ani.cwl supplemental_data->passdata data ignore_all_errors ignore_all_errors fastaval fastaval ignore_all_errors->fastaval ignore_all_errors ignore_all_errors->prepare_input_template ignore_all_errors fasta fasta fasta->fastaval in fasta->prepare_input_template fasta gc_assm_name gc_assm_name gc_assm_name->ping_start instring make_uuid make_uuid make_uuid->ping_start make_uuid uuid_in uuid_in uuid_in->ping_start uuid_in submol submol submol->prepare_input_template submol ani_tax_report_text ani_tax_report_text errors errors uuid_out uuid_out ani_tax_report ani_tax_report Prepare_Seq_entries prepare_seq_entry_input bacterial_kmer bacterial_kmer Prepare_Seq_entries->bacterial_kmer Extract_Kmers_From_Input___entry genomic_source Create Genomic Collection for Bacterial Pipeline, ASN.1 input genomic_source->bacterial_kmer gencoll_asn genomic_source->bacterial_kmer asn_cache prepare_input_template->Prepare_Seq_entries seq_submit prepare_input_template->Prepare_Seq_entries entries prepare_input_template->genomic_source entries prepare_input_template->genomic_source seq_submit prepare_input_template->bacterial_kmer ref_assembly_taxid passdata->genomic_source taxon_db passdata->prepare_input_template taxon_db passdata->bacterial_kmer gc_seq_cache passdata->bacterial_kmer ani_report_transform passdata->bacterial_kmer gc_cache passdata->bacterial_kmer kmer_reference_assemblies passdata->bacterial_kmer kmer_cache_sqlite passdata->bacterial_kmer ANI_cutoff passdata->bacterial_kmer tax_synon passdata->bacterial_kmer taxon_db passdata->bacterial_kmer gcextract2_sqlite bacterial_kmer->ani_tax_report_text bacterial_kmer->errors bacterial_kmer->ani_tax_report bacterial_kmer->ping_stop infile bacterial_kmer->ping_stop infile bacterial_kmer->ping_stop infile ping_start->uuid_out ping_start->genomic_source gc_assm_name ping_start->ping_stop uuid_in
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Inputs

ID Type Title Doc
fasta File
submol File
uuid_in File (Optional)
make_uuid Boolean (Optional)
no_internet Boolean (Optional)
gc_assm_name String
report_usage Boolean
ignore_all_errors Boolean (Optional)
supplemental_data Directory

Steps

ID Runs Label Doc
fastaval
progs/fastaval.cwl (CommandLineTool)
fastaval
passdata
expr/ani.cwl (ExpressionTool)
Split input directory into subpath flows for top level user workflow ani.cwl
ping_stop
progs/pinger.cwl (CommandLineTool)
pinger
ping_start
progs/pinger.cwl (CommandLineTool)
pinger
bacterial_kmer bacterial_kmer
genomic_source Create Genomic Collection for Bacterial Pipeline, ASN.1 input
Prepare_Seq_entries
progs/prepare_seq_entry_input.cwl (CommandLineTool)
prepare_seq_entry_input
prepare_input_template Prepare user input

Prepare user input for NCBI-PGAP pipeline

Outputs

ID Type Label Doc
errors File (Optional)
uuid_out File
ani_tax_report File
ani_tax_report_text File
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Permalink: https://w3id.org/cwl/view/git/a402541b8530f30eab726c160da90a23036847a1/taxcheck.cwl