- 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 | File | ||
final_name | String | ||
readgroups | String[] |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
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 | |
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/43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a/definitions/subworkflows/align_sort_markdup.cwl