Workflow: preprocess fastq
Remove and trim low quality reads from fastq files. Return fasta files with reads passed and reads removed.
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
Unknown workflow license, check
source repository.
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/932da3abed7166bd5a962871386ba2c31d47b85c/CWL/Workflows/preprocess-fastq.workflow.cwl