Workflow: FASTQ Vector Removal
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/11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419/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/6dcc71a3-d27f-44d1-82c3-8190572ee5b0
(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/11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419/workflows/Contamination/fastq-vector-removal.cwl