Workflow: WGS processing workflow for single sample
Fetched 2024-11-24 23:25:08 GMT
Verified with cwltool version 3.1.20230201224320
- 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 |
|---|---|---|---|
| fastq1 | File [FASTQ] | One of set of pair-end FASTQs (R1) | |
| fastq2 | File [FASTQ] | One of set of pair-end FASTQs (R2) | |
| sample | String | Sample Name | |
| 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 | Full list of intervals to operate over |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastqc |
fastqc.cwl
(CommandLineTool)
|
Quality check on FASTQ | |
| samtools-sort |
samtools-sort.cwl
(CommandLineTool)
|
Sort BAM | |
| samtools-index |
samtools-index.cwl
(CommandLineTool)
|
Index BAM | |
| generate-report |
report-wf.cwl
(Workflow)
|
Report generation workflow | |
| haplotypecaller |
scatter-gatk-wf-with-interval.cwl
(Workflow)
|
Scattered variant calling workflow | |
| mark-duplicates |
mark-duplicates.cwl
(CommandLineTool)
|
Mark duplicates using GATK (Picard) | |
| bwamem-samtools-view |
bwamem-samtools-view.cwl
(CommandLineTool)
|
Align FASTQs with BWA |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gvcf | File [VCF] | GVCF generated from GATK Haplotype Caller | |
| qc-zip | File[] | Zip files of FASTQ QC report and associated data | |
| report | File [HTML] | ClinVar variant report | |
| qc-html | File[] [HTML] | FASTQ QC reports |
Permalink:
https://w3id.org/cwl/view/git/e4d896f5f94a9cf7b157cf87d5042e416649d87b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
