Workflow: pipeline-fastq2vcf-multisample.cwl
Fetched 2025-11-06 18:19:06 GMT
Verified with cwltool version 3.1.20221201130942
DNAseq pipeline from fastq to vcf for multiple samples
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- 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 |
|---|---|---|---|
| dbsnp | File (Optional) | ||
| sample | String[] | ||
| library | String[] | ||
| threads | Integer (Optional) | ||
| interval | File (Optional) | ||
| platform | String (Optional) | ||
| readgroup | String[] | ||
| reference | File | ||
| chunk_size | Integer (Optional) | ||
| input_reads | 795a8873042f7a6fbfe26969d98de71a[] | ||
| mark_secondary | Boolean (Optional) | ||
| bqsr_known_sites | File[] | ||
| realign_known_sites | File[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| pipeline |
pipeline-fastq2vcf.cwl
(Workflow)
|
DNAseq pipeline from fastq to vcf |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output | File[] | ||
| bwa_output | File[] | ||
| qcal_output | File[] | ||
| dedup_output | File[] | ||
| realign_output | File[] | ||
| qcal_plot_output | File[] (Optional) | ||
| dedup_metric_output | File[] (Optional) |
Permalink:
https://w3id.org/cwl/view/git/d20382adfe7285cb517a25d95d2bcb7586546e23/pipeline/pipeline-fastq2vcf-multisample.cwl
