Workflow: Run tRNAScan
Fetched 2023-01-04 23:54:00 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
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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-gpipe/pgap/c08fd46e8f715b9b5aa487466705863e4b1829df/GeneMarkS_Software_License.txt
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| taxid | Integer | ||
| seqids | File | ||
| taxon_db | File | ||
| asn_cache | Directory |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| Get_TRNA_model |
../progs/gencode2trnamodel.cwl
(ExpressionTool)
|
||
| Run_tRNAScan_dump |
gpx_qdump.cwl
(CommandLineTool)
|
Run tRNAScan, gather | |
| Run_tRNAScan_wnode |
trnascan_wnode.cwl
(CommandLineTool)
|
Run tRNAScan, execution | |
| Run_tRNAScan_submit |
gpx_qsubmit_trnascan.cwl
(CommandLineTool)
|
Run tRNAScan, scatter | |
| Compute_Gencode_for_trna |
../progs/compute_gencode.cwl
(CommandLineTool)
|
compute_gencode | |
| Run_tRNAScan_trnascan_dump |
trnascan_dump.cwl
(CommandLineTool)
|
Run tRNAScan, transform | |
| Compute_Gencode_int_for_trna |
../progs/file2int.cwl
(ExpressionTool)
|
||
| Compute_Superkingdom_for_trna |
../progs/compute_gencode.cwl
(CommandLineTool)
|
compute_gencode | |
| Compute_Superkingdom_int_for_trna |
../progs/file2int.cwl
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| annots | File |
Permalink:
https://w3id.org/cwl/view/git/c08fd46e8f715b9b5aa487466705863e4b1829df/bacterial_trna/wf_trnascan.cwl
