- 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[] | ||
mills | File | ||
dbsnp_vcf | File | ||
reference | String | ||
readgroups | String[] | ||
known_indels | File |
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.cwl
(CommandLineTool)
|
Sambamba: merge | |
index_bam |
../tools/index_bam.cwl
(CommandLineTool)
|
samtools index | |
apply_bqsr |
../tools/apply_bqsr.cwl
(CommandLineTool)
|
apply BQSR | |
index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
position_sort |
../tools/position_sort.cwl
(CommandLineTool)
|
sort BAM by position |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
final_cram | File |
Permalink:
https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl