Workflow: RNASelector as a CWL workflow
Fetched 2023-01-11 21:21:28 GMT
Verified with cwltool version 3.1.20221201130942
https://doi.org/10.1007/s12275-011-1213-z
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| reads | File [FASTA] | ||
| 5S_model | File [HMMER format] | ||
| 16S_model | File [HMMER format] | ||
| 23S_model | File [HMMER format] | ||
| tRNA_model | File [HMMER format] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| index_reads |
../tools/esl-sfetch-index.cwl
(CommandLineTool)
|
index a sequence file for use by esl-sfetch |
https://github.com/EddyRivasLab/easel |
| find_5S_matches |
../tools/rRNA_selection.cwl
(Workflow)
|
||
| find_16S_matches |
../tools/rRNA_selection.cwl
(Workflow)
|
||
| find_23S_matches |
../tools/rRNA_selection.cwl
(Workflow)
|
||
| find_tRNA_matches |
../tools/tRNA_selection.cwl
(Workflow)
|
||
| mask_rRNA_and_tRNA |
../tools/mask_RNA.cwl
(CommandLineTool)
|
||
| collate_unique_rRNA_hmmer_hits |
../tools/collate_unique_SSU_headers.cwl
(Workflow)
|
||
| collate_unique_tRNA_hmmer_hits |
../tools/collate_unique_SSU_headers.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| 16S_matches | File | ||
| masked_sequences | File |
Permalink:
https://w3id.org/cwl/view/git/85155424fa5654526517369be2fa479a7d4d90de/workflows/rna-selector.cwl
