Workflow: trimmed_fastq
Fetched 2024-11-26 01:53:39 GMT
Verified with cwltool version 3.1.20230201224320
Quality Control and Raw Data trimming
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq1 | File[] | ||
| fastq2 | File[] | ||
| threads_fastp | Integer (Optional) | ||
| threads_fastqc | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastp |
../tools/fastp.cwl
(CommandLineTool)
|
fastp |
Raw Data trimming |
| fastqc_raw |
../tools/fastqc.cwl
(CommandLineTool)
|
fastqc |
Quality Control |
| fastqc_pre_processed |
../tools/fastqc.cwl
(CommandLineTool)
|
fastqc |
Quality Control |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| paired_R1 | File[] | ||
| paired_R2 | File[] | ||
| html_report | File[] | ||
| json_report | File[] | ||
| unpaired_R1 | File[] | ||
| unpaired_R2 | File[] | ||
| fastqc_raw_zip | File[] | ||
| fastqc_raw_html | File[] | ||
| fastqc_paired_zip | File[] | ||
| fastqc_paired_html | File[] |
Permalink:
https://w3id.org/cwl/view/git/cebfad2f456d672052ef8c83f5ff1b4f3b4368e4/structuralvariants/subworkflows/trimmed_fastq.cwl
