Workflow: FASTQ Vector Removal
Fetched 2026-09-28 00:23:41 GMT
Verified with cwltool version 3.1.20230201224320
This workflow clean up vectros from fastq files
- 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/590ed6c9803ba670411c48650bc24deef7863925/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq1 | File | ||
| fastq2 | File (Optional) | ||
| threads | Integer | ||
| vector_fsa | 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 |
| collect_blastdb |
../../tools/basic/files2dir.cwl
(ExpressionTool)
|
files2dir |
Group all input files in a directory |
| extract_read_ids |
fastq-vector-removal.cwl#extract_read_ids/de42851e-febf-48cf-ba6a-c8ca7369d1d1
(CommandLineTool)
|
Extract read IDs | |
| create_clean_fastq |
../../tools/bbmap/filterbyname.cwl
(CommandLineTool)
|
filterbyname |
Filterbyname |
| create_fasta_from_fastq |
../../tools/basic/fastq2fasta.cwl
(CommandLineTool)
|
Create FASTA from FASTQ | |
| create_clean_fasta_from_fastq |
../../tools/basic/fastq2fasta.cwl
(CommandLineTool)
|
Create FASTA from FASTQ |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| clean_fasta_ | File | ||
| fastq1_output | File | ||
| fastq2_output | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/590ed6c9803ba670411c48650bc24deef7863925/workflows/Contamination/fastq-vector-removal.cwl
