Workflow: Align reference proteins plane complete workflow

Fetched 2023-01-10 00:11:05 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs asn_cache asn_cache Sort_Seed_Hits Sort Seed Hits, align_sort asn_cache->Sort_Seed_Hits asn_cache Seed_Search_Compartments Seed Search Compartments asn_cache->Seed_Search_Compartments asn_cache compart_filter_prosplign Filter Protein Seeds; Find ProSplign Alignments asn_cache->compart_filter_prosplign asn_cache Seed_Protein_Alignments Seed Protein Alignments asn_cache->Seed_Protein_Alignments asn_cache Filter_Protein_Alignments Filter Protein Alignments asn_cache->Filter_Protein_Alignments asn_cache Filter_Full_Coverage_Alignments Filter Full-Coverage Alignments asn_cache->Filter_Full_Coverage_Alignments asn_cache all_prots all_prots all_prots->Seed_Protein_Alignments seqids compartments compartments compartments->Seed_Search_Compartments compartments gc_assembly gc_assembly gc_assembly->compart_filter_prosplign gc_assembly go go blastdb_dir blastdb_dir blastdb_dir->Seed_Protein_Alignments blastdb_dir uniColl_asn_cache uniColl_asn_cache uniColl_asn_cache->Sort_Seed_Hits uniColl_asn_cache uniColl_asn_cache->Seed_Search_Compartments uniColl_asn_cache uniColl_asn_cache->compart_filter_prosplign uniColl_asn_cache uniColl_asn_cache->Seed_Protein_Alignments uniColl_asn_cache uniColl_asn_cache->Filter_Protein_Alignments uniColl_asn_cache uniColl_asn_cache->Filter_Full_Coverage_Alignments uniColl_asn_cache tax_sql_file tax_sql_file Compute_Gencode compute_gencode tax_sql_file->Compute_Gencode taxon_db taxid taxid taxid->Compute_Gencode taxid align align align_non_match align_non_match Compute_Gencode_int Compute_Gencode_int Compute_Gencode_int->Seed_Search_Compartments db_gencode Compute_Gencode_int->Seed_Protein_Alignments db_gencode Sort_Seed_Hits->Filter_Full_Coverage_Alignments sorted_seeds cat file concatenation Seed_Search_Compartments->cat file_in_2 compart_filter_prosplign->Filter_Protein_Alignments prosplign Seed_Protein_Alignments->cat file_in_1 cat->Sort_Seed_Hits blast_aligns Filter_Protein_Alignments->align Filter_Protein_Alignments->align_non_match Compute_Gencode->Compute_Gencode_int input Filter_Full_Coverage_Alignments->compart_filter_prosplign seed_hits Filter_Full_Coverage_Alignments->Filter_Protein_Alignments blast_full
Workflow as SVG
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  • Nested Workflows
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  • Inputs/Outputs

Inputs

ID Type Title Doc
go Boolean[]
taxid Integer
all_prots File
asn_cache Directory
blastdb_dir Directory
gc_assembly File
compartments File
tax_sql_file File
uniColl_asn_cache Directory

Steps

ID Runs Label Doc
cat
cat.cwl (CommandLineTool)
file concatenation
Sort_Seed_Hits
align_sort.cwl (CommandLineTool)
Sort Seed Hits, align_sort
Compute_Gencode
../progs/compute_gencode.cwl (CommandLineTool)
compute_gencode
Compute_Gencode_int
../progs/file2int.cwl (ExpressionTool)
Seed_Protein_Alignments
wf_seed_1.cwl (Workflow)
Seed Protein Alignments
Seed_Search_Compartments
wf_seed.cwl (Workflow)
Seed Search Compartments
compart_filter_prosplign Filter Protein Seeds; Find ProSplign Alignments
Filter_Protein_Alignments
wf_align_filter.cwl (Workflow)
Filter Protein Alignments
Filter_Full_Coverage_Alignments
bacterial_protalign_filter.cwl (CommandLineTool)
Filter Full-Coverage Alignments

Outputs

ID Type Label Doc
align File
align_non_match File
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/b38b0070edf910984f29a4a495b5dfa525b8b305/protein_alignment/wf_protein_alignment.cwl