Workflow: duplicated_readgroup_fix.cwl
Fetched 2023-03-31 22:46:24 GMT
Verified with cwltool version 3.1.20230201224320
- 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 |
|---|---|---|---|
| bam_md5 | String | ||
| bam_url | String | ||
| job_uuid | String | ||
| aws_config | File | ||
| s3_profile | String | ||
| s3_endpoint | String | ||
| new_readgroups | String[] | ||
| upload_bam_url | String | ||
| readgroups_to_replace | String[] | ||
| aws_shared_credentials | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| download_bam |
download_check.cwl
(Workflow)
|
||
| get_bam_header |
../../tools/harmonization/get_bam_header.cwl
(CommandLineTool)
|
||
| samtools_index |
../../tools/harmonization/samtools_index.cwl
(CommandLineTool)
|
||
| create_new_header |
../../tools/harmonization/readgroup_replace.cwl
(CommandLineTool)
|
||
| samtools_reheader |
../../tools/harmonization/samtools_reheader.cwl
(CommandLineTool)
|
||
| upload_reheadered_bam |
../../tools/utils/awscli_upload.cwl
(CommandLineTool)
|
||
| upload_reheadered_bam_index |
../../tools/utils/awscli_upload.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| time_metrics | File | ||
| reheadered_bam | File |
Permalink:
https://w3id.org/cwl/view/git/286bce04c474d28bddeb7dbe43ab8d59919fe855/genomel/cwl/workflows/utils/duplicated_readgroup_fix.cwl
