Workflow: contamination_foreign_chromosome
Fetched 2025-04-29 13:45:28 GMT
Verified with cwltool version 3.1.20230201224320
This workflow detect and remove foreign chromosome 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 |
|---|---|---|---|
| blastdb | Directory | ||
| threads | Integer | ||
| blastdb_name | String | ||
| trans_fsa_gz | File | ||
| perc_identity | Float |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| blastn |
../../tools/blast/blastn.cwl
(CommandLineTool)
|
BlastN |
NCBI BlastN Nucleotide-Nucleotide BLAST |
| uncompress_noequal |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| blastn_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49/workflows/Contamination/contamination-foreign-chromosome-blastn.cwl
