Workflow: ribosomal_cleanup
Fetched 2023-01-09 22:05:21 GMT
Verified with cwltool version 3.1.20221201130942
This workflow detect and remove ribosomal 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/3247592a89deafaa0d9c5910a1cb1d000ef9b098/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| threads | Integer | ||
| ribo_fsa | File | ||
| trans_fsa_gz | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter_blast |
../../tools/python/filter-fasta-by-blast.cwl
(CommandLineTool)
|
contamination_detection |
This tools remove contamination using a Blast TSV file |
| ribo_blastdb |
../../tools/blast/makeblastdb.cwl
(CommandLineTool)
|
makeblastdb |
NCBI makeblastdb |
| collect_blastdb |
../../tools/basic/files2dir.cwl
(ExpressionTool)
|
files2dir |
Group all input files in a directory |
| ribosomal_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 |
|---|---|---|---|
| filtered_fsa | File | ||
| filtered_ids | File | ||
| ribosomal_blastn_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/3247592a89deafaa0d9c5910a1cb1d000ef9b098/workflows/Contamination/ribosomal-cleanup.cwl
