Workflow: Preprocess fastq
Fetched 2023-01-13 15:22:28 GMT
Verified with cwltool version 3.1.20221201130942
Remove and trim low quality reads from fastq files. Return fasta files with reads passed and reads removed.
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 2-clause "Simplified" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| jobid | String | ||
| maxLqb | Integer | ||
| minQual | Integer | ||
| minLength | Integer | ||
| sequences | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter |
../Tools/fastq-mcf.tool.cwl
(CommandLineTool)
|
fastq-mcf |
fastq quality trimmer >fastq-mcf 'n/a' <input> -S -k 0 -l <minLength> --max-ns <maxLqb> -q <minQual> -w <window> -o <outName> |
| adapterTrim |
../Tools/autoskewer.tool.cwl
(CommandLineTool)
|
autoskewer |
detect and trim adapter sequences from reads >autoskewer.py -t <runtime.tmpdir> -i <input> -o <outName> -l <outLog> |
| passed2fasta |
../Tools/seqUtil.tool.cwl
(CommandLineTool)
|
seqUtil |
Utility tool for various sequence file transformations. |
| removed2fasta |
../Tools/seqUtil.tool.cwl
(CommandLineTool)
|
seqUtil |
Utility tool for various sequence file transformations. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| passed | File | ||
| removed | File | ||
| trimmed | File |
Permalink:
https://w3id.org/cwl/view/git/7b1df2ecce5a8727f2c546c5baa45c919edd8a76/CWL/Workflows/preprocess-fastq.workflow.cwl
