Workflow: transcriptome_cleanup
Fetched 2023-01-24 06:02:28 GMT
Verified with cwltool version 3.1.20221201130942
This workflow detect and remove vector, duplicate and contamination from a transcriptome 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/de6380d83f9209e95559e66cf64ded3bf0e410ea/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| evalue | Float | ||
| threads | Integer | ||
| min_length | Integer | ||
| vector_fsa | File | ||
| trans_fsa_gz | File | ||
| total_per_file | Integer | ||
| vector_bp_cutoff | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| split_fasta |
../../tools/python/split-fasta.cwl
(CommandLineTool)
|
split_fasta |
Split fasta file in multiple files |
| 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 |
| duplicate_blastn |
../../tools/blast/blastn.cwl
(CommandLineTool)
|
BlastN |
NCBI BlastN Nucleotide-Nucleotide BLAST |
| duplicate_blastdb |
../../tools/blast/makeblastdb.cwl
(CommandLineTool)
|
makeblastdb |
NCBI makeblastdb |
| duplicate_removal |
../../tools/python/duplicate-removal.cwl
(CommandLineTool)
|
duplicate_removal |
This tools remove duplicate sequences |
| equal_seq_removal |
../../tools/python/equal-removal.cwl
(CommandLineTool)
|
equal_removal |
This tools remove equal sequences |
| uncompress_no_vect |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| uncompress_noequal |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| collect_duplicate_blastdb |
../../tools/basic/files2dir.cwl
(ExpressionTool)
|
files2dir |
Group all input files in a directory |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| split_fasta_fsa | File[] |
Permalink:
https://w3id.org/cwl/view/git/de6380d83f9209e95559e66cf64ded3bf0e410ea/workflows/Annotation/transcriptome-cleanup.cwl
