Workflow: mito_cleanup
Fetched 2025-04-30 03:03:49 GMT
Verified with cwltool version 3.1.20230201224320
This workflow detect and remove Mitochondrial 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 | ||
| min_length | Integer | ||
| trans_fsa_gz | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| mito_blastn |
../../tools/blast/blastn.cwl
(CommandLineTool)
|
BlastN |
NCBI BlastN Nucleotide-Nucleotide BLAST |
| filter_blast |
../../tools/python/filter-fasta-by-blast.cwl
(CommandLineTool)
|
contamination_detection |
This tools remove contamination using a Blast TSV file |
| collect_blastdb |
../../tools/basic/files2dir.cwl
(ExpressionTool)
|
files2dir |
Group all input files in a directory |
| download_blastdb |
../../tools/blast/update_blastdb.cwl
(CommandLineTool)
|
BlastN |
NCBI BlastN Nucleotide-Nucleotide BLAST |
| uncompress_noequal |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filtered_fsa | File | ||
| filtered_ids | File | ||
| mito_blastn_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49/workflows/Contamination/mitochondrial-cleanup.cwl
