Workflow: bwamem-gatk-report-wf.cwl
Fetched 2023-01-04 01:27:33 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq1 | File | ||
| fastq2 | File | ||
| sample | String | ||
| headhtml | File | ||
| tailhtml | File | ||
| reference | File | ||
| clinvarvcf | File | ||
| knownsites | File | ||
| reportfunc | File | ||
| scattercount | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastqc |
fastqc.cwl
(CommandLineTool)
|
Quality check on fastq data using FastQC | |
| samtools-sort |
samtools-sort.cwl
(CommandLineTool)
|
Sorting Bam file | |
| samtools-index |
samtools-index.cwl
(CommandLineTool)
|
Indexing Bam File | |
| generate-report |
report-wf.cwl
(Workflow)
|
||
| haplotypecaller |
scatter-gatk-wf-with-interval.cwl
(Workflow)
|
||
| mark-duplicates |
mark-duplicates.cwl
(CommandLineTool)
|
Marking Duplicates using Picard | |
| bwamem-samtools-view |
bwamem-samtools-view.cwl
(CommandLineTool)
|
Realigning fastqs and converting output to bam |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gvcf | File | ||
| qc-zip | File[] | ||
| report | File | ||
| qc-html | File[] |
Permalink:
https://w3id.org/cwl/view/git/36de0d12e1cc88d0fd7d6b401df6c6e403f8c809/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
