Workflow: pipeline-fastq2vcf-parallel-bwa.cwl
Fetched 2025-07-13 22:56:41 GMT
Verified with cwltool version 3.1.20221201130942
DNAseq pipeline from fastq to vcf
- Selected
- |
- 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 (Optional) | ||
| threads | Integer (Optional) | ||
| interval | File (Optional) | ||
| platform | String (Optional) | ||
| readgroup | String[] | ||
| reference | File | ||
| chunk_size | Integer (Optional) | ||
| input_reads | e69b8b3652ca76afcae5241ce92c2c38[] | ||
| output_file | String | ||
| bwa_output_bam | String | ||
| mark_secondary | Boolean (Optional) | ||
| bqsr_known_sites | File[] | ||
| dedup_output_bam | String | ||
| qcal_output_file | String | ||
| realign_output_bam | String | ||
| realign_known_sites | File[] | ||
| dedup_metrics_output_file | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| hc |
../algo/hc.cwl
(CommandLineTool)
|
||
| bwa |
../algo/bwa-mem-sort.cwl
(CommandLineTool)
|
||
| bqsr |
../stage/bqsr-flow.cwl
(Workflow)
|
Run BQSR pre+post+plot flow |
|
| dedup |
../stage/dedup-2-pass.cwl
(Workflow)
|
run 2-pass dedup: algo LocusCollector + algo Dedup sequentially |
|
| realign |
../algo/realign.cwl
(CommandLineTool)
|
||
| bam_merge |
../algo/bam-merge.cwl
(CommandLineTool)
|
merge sorted bam files. If input bam files are in the order of coordinate, and no overlap, mergemode 10 can be used |
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_metrics_output | File (Optional) | ||
| qcal_plot_csv_output | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/d20382adfe7285cb517a25d95d2bcb7586546e23/pipeline/pipeline-fastq2vcf-parallel-bwa.cwl
