Workflow: vector_cleanup
Fetched 2023-01-03 20:21:36 GMT
Verified with cwltool version 3.1.20221201130942
This workflow detect and remove vectors 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/11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| threads | Integer | ||
| min_length | Integer | ||
| vector_fsa | File | ||
| trans_fsa_gz | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| vector_blastn |
../../tools/blast/blastn.cwl
(CommandLineTool)
|
BlastN |
NCBI BlastN Nucleotide-Nucleotide BLAST |
| vector_blastdb |
../../tools/blast/makeblastdb.cwl
(CommandLineTool)
|
makeblastdb |
NCBI makeblastdb |
| vector_removal |
../../tools/python/vector-removal.cwl
(CommandLineTool)
|
vector_removal |
This tools detect vectors from a Blast TSV file |
| collect_blastdb |
../../tools/basic/files2dir.cwl
(ExpressionTool)
|
files2dir |
Group all input files in a directory |
| uncompress_noequal |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| equal_seq_removal_1 |
../../tools/python/equal-removal.cwl
(CommandLineTool)
|
equal_removal |
This tools remove equal sequences |
| equal_seq_removal_2 |
../../tools/python/equal-removal.cwl
(CommandLineTool)
|
equal_removal |
This tools remove equal sequences |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| vector_cont | File | ||
| vector_clean | File | ||
| vector_blastn_tsv | File | ||
| equal_seq_removal_1_tsv | File | ||
| equal_seq_removal_2_fsa | File | ||
| equal_seq_removal_2_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419/workflows/Contamination/vector-cleanup.cwl
