Workflow: etl_http.cwl
Fetched 2023-01-14 08:43:33 GMT
Verified with cwltool version 3.1.20221201130942
- 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 |
|---|---|---|---|
| job_uuid | String | ||
| gdc_token | File | ||
| thread_count | Long | ||
| input_bam_gdc_id | String | ||
| known_snp_gdc_id | String | ||
| input_bam_file_size | Long | ||
| known_snp_file_size | Long | ||
| reference_fa_gdc_id | String | ||
| reference_sa_gdc_id | String | ||
| reference_amb_gdc_id | String | ||
| reference_ann_gdc_id | String | ||
| reference_bwt_gdc_id | String | ||
| reference_fai_gdc_id | String | ||
| reference_pac_gdc_id | String | ||
| reference_dict_gdc_id | String | ||
| known_snp_index_gdc_id | String | ||
| reference_fa_file_size | Long | ||
| reference_sa_file_size | Long | ||
| reference_amb_file_size | Long | ||
| reference_ann_file_size | Long | ||
| reference_bwt_file_size | Long | ||
| reference_fai_file_size | Long | ||
| reference_pac_file_size | Long | ||
| reference_dict_file_size | Long | ||
| known_snp_index_file_size | Long |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| transform |
transform.cwl
(Workflow)
|
||
| extract_bam |
../../tools/gdc_get_object.cwl
(CommandLineTool)
|
||
| root_fasta_files |
../../tools/root_fasta_dnaseq.cwl
(CommandLineTool)
|
||
| extract_known_snp |
../../tools/gdc_get_object.cwl
(CommandLineTool)
|
||
| extract_reference_fa |
../../tools/gdc_get_object.cwl
(CommandLineTool)
|
||
| extract_reference_sa |
../../tools/gdc_get_object.cwl
(CommandLineTool)
|
||
| root_known_snp_files |
../../tools/root_vcf.cwl
(CommandLineTool)
|
||
| extract_reference_amb |
../../tools/gdc_get_object.cwl
(CommandLineTool)
|
||
| extract_reference_ann |
../../tools/gdc_get_object.cwl
(CommandLineTool)
|
||
| extract_reference_bwt |
../../tools/gdc_get_object.cwl
(CommandLineTool)
|
||
| extract_reference_fai |
../../tools/gdc_get_object.cwl
(CommandLineTool)
|
||
| extract_reference_pac |
../../tools/gdc_get_object.cwl
(CommandLineTool)
|
||
| extract_reference_dict |
../../tools/gdc_get_object.cwl
(CommandLineTool)
|
||
| extract_known_snp_index |
../../tools/gdc_get_object.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File | ||
| sqlite | File |
Permalink:
https://w3id.org/cwl/view/git/58af8583ab04b8836777745a2116a2e79f9b441b/workflows/dnaseq/etl_http.cwl
