Workflow: contaminant_cleanup
Fetched 2026-07-06 01:18:02 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/590ed6c9803ba670411c48650bc24deef7863925/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| threads | Integer | ||
| trans_fsa | File | ||
| min_length | Integer | ||
| sequence_chunk | Integer | ||
| contaminant_fsa | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| collect_blastdb |
../../tools/basic/files2dir.cwl
(ExpressionTool)
|
files2dir |
Group all input files in a directory |
| contaminant_blastn |
../../tools/blast/blastn.cwl
(CommandLineTool)
|
BlastN |
NCBI BlastN Nucleotide-Nucleotide BLAST |
| contaminant_blastdb |
../../tools/blast/makeblastdb.cwl
(CommandLineTool)
|
makeblastdb |
NCBI makeblastdb |
| contamination_removal |
../../tools/python/contaminant-removal.cwl
(CommandLineTool)
|
contaminant_removal |
This tools detect contaminants from a Blast TSV file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| contaminant_blastn_tsv | File | ||
| contamination_removal_fsa | File | ||
| contamination_removal_cont | File |
Permalink:
https://w3id.org/cwl/view/git/590ed6c9803ba670411c48650bc24deef7863925/workflows/Contamination/fastq-contaminant-cleanup.cwl
