Workflow: contaminant_cleanup
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 | ||
trans_fsa | File | ||
min_length | Integer | ||
contaminant_fsa | File |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
collect_blastdb |
../../tools/basic/files2dir.cwl
(ExpressionTool)
|
files2dir |
Group all input files in a directory |
equal_seq_removal |
../../tools/python/equal-removal.cwl
(CommandLineTool)
|
equal_removal |
This tools remove equal sequences |
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 |
---|---|---|---|
equal_seq_removal_fsa | File | ||
equal_seq_removal_tsv | File | ||
contaminant_blastn_tsv | File | ||
contamination_removal_cont | File |
Permalink:
https://w3id.org/cwl/view/git/1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49/workflows/Contamination/contaminant-cleanup.cwl