Workflow: fastq2fasta.cwl
Fetched 2023-01-04 22:56:30 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| threads | Integer | ||
| metadata | File (Optional) | ||
| ref_fasta | File | ||
| fastq_forward | File | ||
| fastq_reverse | File (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bwa-mem |
bwa-mem.cwl
(CommandLineTool)
|
string |
|
| samtools-sort |
samtools-sort.cwl
(CommandLineTool)
|
samtools sort, sort given bam file |
|
| samtools-view |
samtools-view.cwl
(CommandLineTool)
|
samtools view to convert sam format to bam format |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| out_fasta | File | ||
| out_metadata | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/967e06fd4e5847e326a9b77ff3f0354aff69329a/cwl/fastq2fasta/fastq2fasta.cwl
