- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
bams | File[] | ||
reference | String | ||
final_name | String | ||
readgroups | String[] | ||
bqsr_intervals | String[] (Optional) | ||
bqsr_known_sites | File[] |
One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
bqsr |
../tools/bqsr.cwl
(CommandLineTool)
|
create BQSR table | |
align |
align.cwl
(Workflow)
|
Unaligned to aligned BAM | |
merge |
../tools/merge_bams_samtools.cwl
(CommandLineTool)
|
Samtools: merge | |
index_bam |
../tools/index_bam.cwl
(CommandLineTool)
|
samtools index | |
name_sort |
../tools/name_sort.cwl
(CommandLineTool)
|
sort BAM by name | |
apply_bqsr |
../tools/apply_bqsr.cwl
(CommandLineTool)
|
apply BQSR | |
mark_duplicates_and_sort |
../tools/mark_duplicates_and_sort.cwl
(CommandLineTool)
|
Mark duplicates and Sort |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
final_bam | File | ||
mark_duplicates_metrics_file | File |
Permalink:
https://w3id.org/cwl/view/git/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/subworkflows/bam_to_bqsr.cwl