Workflow: BAM to BEDPE
Fetched 2026-07-21 07:46:59 GMT
Verified with cwltool version 3.1.20230201224320
Comvert BAM to BEDPE and compress the output
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/ncbi/cwl-ngs-workflows-cbb/0207b0171ab142dfb85db9c39050c5b4be51dd9e/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bam | File |
BAM file to be analyzed |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gzip |
../../tools/basic/gzip.cwl
(CommandLineTool)
|
gzip |
Compress files |
| bamtobed |
../../tools/bedtools/bedtools-bamtobed.cwl
(CommandLineTool)
|
bedtools-bamtobed |
The bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| out | File |
Permalink:
https://w3id.org/cwl/view/git/0207b0171ab142dfb85db9c39050c5b4be51dd9e/workflows/File-formats/bamtobedpe-gzip.cwl
