Workflow: WGS processing workflow scattered over samples
Fetched 2023-01-10 18:01:02 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:
GNU Affero General Public License v3.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastqdir | Directory | Directory of paired FASTQ files | |
| headhtml | File [HTML] | Header for HTML report | |
| tailhtml | File [HTML] | Footer for HTML report | |
| reference | File [FASTA] | Reference genome | |
| clinvarvcf | File [VCF] | Reference VCF for ClinVar | |
| reportfunc | File | Function used to create HTML report | |
| knownsites1 | File [VCF] | VCF of known SNPS sites for BQSR | |
| knownsites2 | File [VCF] | VCF of known indel sites for BQSR | |
| scattercount | String | Desired split for variant calling | |
| fullintervallist | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| getfastq |
helper/getfastq.cwl
(ExpressionTool)
|
Find matching FASTQ pairs | |
| bwamem-gatk-report |
helper/bwamem-gatk-report-wf.cwl
(Workflow)
|
WGS processing workflow for single sample |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gvcf | File[] [VCF] | GVCFs generated from GATK | |
| report | File[] [HTML] | ClinVar variant reports |
Permalink:
https://w3id.org/cwl/view/git/d147d1d1fafeeea06bd09d9479337b0f5aab43b0/WGS-processing/cwl/wgs-processing-wf.cwl
