Workflow: Align reference proteins plane complete workflow

Fetched 2023-01-10 02:18:18 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs uniColl_asn_cache uniColl_asn_cache compart_filter_prosplign Filter Protein Seeds; Find ProSplign Alignments uniColl_asn_cache->compart_filter_prosplign uniColl_asn_cache Seed_Protein_Alignments Seed Protein Alignments uniColl_asn_cache->Seed_Protein_Alignments uniColl_asn_cache Sort_Seed_Hits Sort Seed Hits, align_sort uniColl_asn_cache->Sort_Seed_Hits uniColl_asn_cache Seed_Search_Compartments Seed Search Compartments uniColl_asn_cache->Seed_Search_Compartments uniColl_asn_cache Filter_Protein_Alignments Filter Protein Alignments uniColl_asn_cache->Filter_Protein_Alignments uniColl_asn_cache Filter_Full_Coverage_Alignments Filter Full-Coverage Alignments uniColl_asn_cache->Filter_Full_Coverage_Alignments uniColl_asn_cache blastdb_dir blastdb_dir blastdb_dir->Seed_Protein_Alignments blastdb_dir asn_cache asn_cache asn_cache->compart_filter_prosplign asn_cache asn_cache->Seed_Protein_Alignments asn_cache asn_cache->Sort_Seed_Hits asn_cache asn_cache->Seed_Search_Compartments asn_cache asn_cache->Filter_Protein_Alignments asn_cache asn_cache->Filter_Full_Coverage_Alignments asn_cache compartments compartments compartments->Seed_Search_Compartments compartments taxid taxid Compute_Gencode compute_gencode taxid->Compute_Gencode taxid go go tax_sql_file tax_sql_file tax_sql_file->Compute_Gencode taxon_db gc_assembly gc_assembly gc_assembly->compart_filter_prosplign gc_assembly all_prots all_prots all_prots->Seed_Protein_Alignments seqids align_non_match align_non_match align align compart_filter_prosplign->Filter_Protein_Alignments prosplign cat file concatenation cat->Sort_Seed_Hits blast_aligns Compute_Gencode_int Compute_Gencode_int Compute_Gencode->Compute_Gencode_int input Seed_Protein_Alignments->cat file_in_1 Sort_Seed_Hits->Filter_Full_Coverage_Alignments sorted_seeds Seed_Search_Compartments->cat file_in_2 Filter_Protein_Alignments->align_non_match Filter_Protein_Alignments->align Compute_Gencode_int->Seed_Protein_Alignments db_gencode Compute_Gencode_int->Seed_Search_Compartments db_gencode 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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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
Permalink: https://w3id.org/cwl/view/git/a402541b8530f30eab726c160da90a23036847a1/protein_alignment/wf_protein_alignment.cwl