Workflow: fastq2fasta.cwl
Fetched 2023-01-10 14:14:48 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:
Apache License 2.0
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 | ||
| sample_id | String | ||
| 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/4f30e506055acb788a1ff1bbcb6359c4413a4eab/workflows/fastq2fasta/fastq2fasta.cwl
