Workflow: Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)

Fetched 2023-01-14 17:39:52 GMT
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Inputs

ID Type Title Doc
models1 File Run GeneMark Training/models
hmms_tab File
raw_seqs File
taxon_db File
wp_hashes File
AntiFamLib Directory
annotation File Resolve Annotation Conflicts/annotation
hmm_aligns File Map HMM Hits/align
hmm_params File (Optional)
thresholds File
prot_aligns File Filter Protein Alignments I/align
genemark_path Directory
naming_sqlite File
uniColl_cache Directory
selenoproteins Directory
sequence_cache Directory
selenocysteines_db String
naming_hmms_combined Directory
scatter_gather_nchunks String

Steps

ID Runs Label Doc
Name_by_WPs
../progs/identify_wp.cwl (CommandLineTool)
identify_wp
Run_GeneMark
../progs/genemark.cwl (CommandLineTool)
genemark
Run_GeneMark_Post
../progs/genemark_post.cwl (CommandLineTool)
genemark_post
Search_Naming_HMMs
PGAP_plus_ab_initio
../progs/bact_entries_merge.cwl (CommandLineTool)
bact_entries_merge
Extract_Model_Proteins protein_extract
Good_ab_initio_proteins
../progs/set_operation.cwl (CommandLineTool)
set_operation
Extract_ab_initio_Proteins protein_extract
Good_ab_initio_annotations
../progs/bact_filter_preserved.cwl (CommandLineTool)
bact_filter_preserved
Search_ab_initio_for_AntiFam
Assign_Naming_HMM_to_Proteins
../progs/assign_hmm.cwl (CommandLineTool)
assign_hmm
Find_Best_Evidence_Alignments
../progs/bact_best_evidence_alignments.cwl (CommandLineTool)
bact_best_evidence_alignments
ab_initio_AntiFam_tainted_proteins
../progs/reduce.cwl (CommandLineTool)
reduce

Outputs

ID Type Label Doc
Name_by_WPs_names File
Run_GeneMark_Post_models File
Extract_Model_Proteins_lds2 File
Search_Naming_HMMs_hmm_hits File
Extract_Model_Proteins_seqids File
PGAP_plus_ab_initio_annotation File
Extract_Model_Proteins_proteins File
Find_Best_Evidence_Alignments_aligns File goes to protein_alignment/Seed Search Compartments/compartments
Assign_Naming_HMM_to_Proteins_assignments File
Permalink: https://w3id.org/cwl/view/git/1a6b9e5dea09caa0debbaff30ca39005dfa5e4d4/bacterial_annot/wf_bacterial_annot_pass3.cwl