Workflow: Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)

Fetched 2023-01-14 17:28:00 GMT
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Inputs

ID Type Title Doc
go Boolean[]
inseq File
hmm_path Directory
hmms_tab File
asn_cache Directory
nogenbank Boolean
thresholds File
trna_annots File
ncrna_annots File
genemark_path Directory
naming_sqlite File
uniColl_cache Directory
selenoproteins Directory
selenocysteines_db String
Execute_CRISPRs_annots File
scatter_gather_nchunks String
Generate_16S_rRNA_Annotation_annotation File
Generate_23S_rRNA_Annotation_annotation File
Post_process_CMsearch_annotations_annots_5S File

Steps

ID Runs Label Doc
Get_ORFs
../progs/gp_getorf.cwl (CommandLineTool)
gp_getorf
Map_HMM_Hits
bacterial_hit_mapping.cwl (CommandLineTool)
Map HMM Hits
Search_All_HMMs_I
Get_off_frame_ORFs
get_off_frame_orfs.cwl (CommandLineTool)
Get off-frame ORFs
Extract_ORF_Proteins protein_extract
Run_GeneMark_Training
../progs/genemark_training.cwl (CommandLineTool)
genemark_training
Run_GeneMark_Training_post
../progs/genemark_post.cwl (CommandLineTool)
genemark_post
Resolve_Annotation_Conflicts
../progs/bacterial_resolve_conflicts.cwl (CommandLineTool)
bacterial_resolve_conflicts

Outputs

ID Type Label Doc
lds2 File
aligns File
seqids File
models1 File
outseqs File
hmm_hits File
prot_ids File
proteins File
annotation File
out_hmm_params File (Optional)
protein_aligns File
Permalink: https://w3id.org/cwl/view/git/1a6b9e5dea09caa0debbaff30ca39005dfa5e4d4/bacterial_annot/wf_bacterial_annot_pass1.cwl