Workflow: Align reference proteins plane complete workflow

Fetched 2023-01-14 17:54:02 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 compart_filter_prosplign Filter Protein Seeds I; Find ProSplign Alignments I asn_cache->compart_filter_prosplign asn_cache Filter_Full_Coverage_Alignments_I Filter Full-Coverage Alignments I asn_cache->Filter_Full_Coverage_Alignments_I asn_cache Filter_Protein_Alignments_I Filter Protein Alignments I asn_cache->Filter_Protein_Alignments_I asn_cache Seed_Search_Compartments Seed Search Compartments asn_cache->Seed_Search_Compartments asn_cache Seed_Protein_Alignments Seed Protein Alignments I asn_cache->Seed_Protein_Alignments asn_cache taxid taxid Get_Proteins Get Proteins, bacterial_prot_src taxid->Get_Proteins taxid Compute_Gencode compute_gencode taxid->Compute_Gencode taxid go go naming_sqlite naming_sqlite naming_sqlite->Get_Proteins naming_sqlite compartments compartments compartments->Seed_Search_Compartments compartments tax_sql_file tax_sql_file tax_sql_file->Get_Proteins tax_sql_file tax_sql_file->Compute_Gencode taxon_db uniColl_asn_cache uniColl_asn_cache uniColl_asn_cache->Sort_Seed_Hits uniColl_asn_cache uniColl_asn_cache->Get_Proteins uniColl_asn_cache uniColl_asn_cache->compart_filter_prosplign uniColl_asn_cache uniColl_asn_cache->Filter_Full_Coverage_Alignments_I uniColl_asn_cache uniColl_asn_cache->Filter_Protein_Alignments_I uniColl_asn_cache uniColl_asn_cache->Seed_Search_Compartments uniColl_asn_cache uniColl_asn_cache->Seed_Protein_Alignments uniColl_asn_cache gc_assembly gc_assembly gc_assembly->compart_filter_prosplign gc_assembly blastdb_dir blastdb_dir blastdb_dir->Seed_Protein_Alignments blastdb_dir align align align_non_match align_non_match universal_clusters universal_clusters Sort_Seed_Hits->Filter_Full_Coverage_Alignments_I sorted_seeds Compute_Gencode_int Compute_Gencode_int Compute_Gencode_int->Seed_Search_Compartments db_gencode Compute_Gencode_int->Seed_Protein_Alignments db_gencode Get_Proteins->universal_clusters Get_Proteins->Seed_Protein_Alignments seqids compart_filter_prosplign->Filter_Protein_Alignments_I prosplign Filter_Full_Coverage_Alignments_I->compart_filter_prosplign seed_hits Filter_Full_Coverage_Alignments_I->Filter_Protein_Alignments_I blast_full Compute_Gencode->Compute_Gencode_int input cat file concatenation cat->Sort_Seed_Hits blast_aligns Filter_Protein_Alignments_I->align Filter_Protein_Alignments_I->align_non_match Seed_Search_Compartments->cat file_in_2 Seed_Protein_Alignments->cat file_in_1 default1 "1G" default1->Sort_Seed_Hits limit_mem default2 true default2->Compute_Gencode gencode
Workflow as SVG
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Inputs

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

Steps

ID Runs Label Doc
cat
cat.cwl (CommandLineTool)
file concatenation
Get_Proteins
bacterial_prot_src.cwl (CommandLineTool)
Get Proteins, bacterial_prot_src
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 I
Seed_Search_Compartments
wf_seed.cwl (Workflow)
Seed Search Compartments
compart_filter_prosplign Filter Protein Seeds I; Find ProSplign Alignments I
Filter_Protein_Alignments_I
wf_align_filter.cwl (Workflow)
Filter Protein Alignments I
Filter_Full_Coverage_Alignments_I
bacterial_protalign_filter.cwl (CommandLineTool)
Filter Full-Coverage Alignments I

Outputs

ID Type Label Doc
align File
align_non_match File
universal_clusters File
Permalink: https://w3id.org/cwl/view/git/5ec226c941562124032ca6861bc8d1aeabf9d91a/protein_alignment/wf_protein_alignment.cwl