Workflow: Unaligned BAM to BQSR and VCF
Fetched 2024-05-05 16:51:00 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:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bams | File[] | ||
| dbsnp | File | ||
| mills | File | ||
| reference | String | ||
| readgroups | String[] | ||
| known_indels | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bqsr |
exome_alignment_packed.cwl#bqsr.cwl
(CommandLineTool)
|
create BQSR table | |
| align |
exome_alignment_packed.cwl#align.cwl
(Workflow)
|
Unaligned to aligned BAM | |
| merge |
exome_alignment_packed.cwl#merge.cwl
(CommandLineTool)
|
merge BAMs | |
| name_sort |
exome_alignment_packed.cwl#name_sort.cwl
(CommandLineTool)
|
sort BAM by name | |
| apply_bqsr |
exome_alignment_packed.cwl#apply_bqsr.cwl
(CommandLineTool)
|
apply BQSR | |
| index_cram |
exome_alignment_packed.cwl#index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| bam_to_cram |
exome_alignment_packed.cwl#bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| mark_duplicates_and_sort |
exome_alignment_packed.cwl#mark_duplicates_and_sort.cwl
(CommandLineTool)
|
mark duplicates and sort |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_cram | File |
Permalink:
https://w3id.org/cwl/view/git/0ae2468ab2ba0b9a196c2aa89b580555750bf0f6/workflows/hello/exome_alignment_packed.cwl?part=workflow.cwl_2
