Workflow: contamination_cleanup
Fetched 2025-04-30 00:32:08 GMT
Verified with cwltool version 3.1.20230201224320
This workflow detect and remove contamination from a DNA fasta file
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/ncbi/cwl-ngs-workflows-cbb/master/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| threads | Integer | ||
| ribo_fsa | File | ||
| trans_fsa | File | ||
| min_length | Integer | ||
| contaminant_fsa | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| ribosomal_removal |
ribosomal-cleanup.cwl
(Workflow)
|
ribosomal_cleanup |
This workflow detect and remove ribosomal from a DNA fasta file |
| contamination_removal |
contaminant-cleanup.cwl
(Workflow)
|
contaminant_cleanup |
This workflow detect and remove contamination from a DNA fasta file |
| mitochondrial_removal |
mitochondrial-cleanup.cwl
(Workflow)
|
mito_cleanup |
This workflow detect and remove Mitochondrial from a DNA fasta file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| equal_seq_removal_fsa | File | ||
| equal_seq_removal_tsv | File | ||
| ribosomal_removal_fsa | File | ||
| ribosomal_removal_tsv | File | ||
| contaminant_blastn_tsv | File | ||
| ribosomal_removal_blastn | File | ||
| mitochondrial_removal_fsa | File | ||
| mitochondrial_removal_tsv | File | ||
| contamination_removal_cont | File | ||
| mitochondrial_removal_blastn | File |
Permalink:
https://w3id.org/cwl/view/git/1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49/workflows/Contamination/contamination-cleanup.cwl
