Workflow: Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)
Fetched 2024-11-23 19:49:46 GMT
Verified with cwltool version 3.1.20230201224320
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/ncbi/pgap/test/LICENSE.md
Note that the tools invoked by the workflow may have separate licenses.
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 | String | ||
| naming_sqlite | File | ||
| uniColl_cache | Directory | ||
| selenoproteins | Directory | ||
| selenoproteins_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)
|
bacterial_hit_mapping | |
| Search_All_HMMs |
../task_types/tt_hmmsearch_wnode.cwl
(Workflow)
|
||
| Get_off_frame_ORFs |
get_off_frame_orfs.cwl
(CommandLineTool)
|
Get off-frame ORFs | |
| Extract_ORF_Proteins |
../progs/protein_extract.cwl
(Workflow)
|
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/5b498b4c4f17bb8f17e6886aa4c5661d7aba34fc/bacterial_annot/wf_bacterial_annot_pass1.cwl
