Workflow: etl.cwl
Fetched 2023-01-11 21:22:44 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 |
|---|---|---|---|
| bam_name | String | ||
| job_uuid | String | ||
| start_token | File (Optional) | ||
| thread_count | Long | ||
| bioclient_config | File | ||
| known_snp_gdc_id | String | ||
| run_markduplicates | 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 | ||
| bioclient_load_bucket | 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 | ||
| readgroups_bam_uuid_list | https://w3id.org/cwl/view/git/3fa737f9162bbfbdbc243a3b1ff7c8e110875eba/tools/readgroup.yml#readgroups_bam_uuid[] | ||
| reference_dict_file_size | Long | ||
| capture_kit_set_uuid_list | https://w3id.org/cwl/view/git/3fa737f9162bbfbdbc243a3b1ff7c8e110875eba/tools/capture_kit.yml#capture_kit_set_uuid[] | ||
| known_snp_index_file_size | Long | ||
| amplicon_kit_set_uuid_list | https://w3id.org/cwl/view/git/3fa737f9162bbfbdbc243a3b1ff7c8e110875eba/tools/amplicon_kit.yml#amplicon_kit_set_uuid[] | ||
| readgroup_fastq_pe_uuid_list | https://w3id.org/cwl/view/git/3fa737f9162bbfbdbc243a3b1ff7c8e110875eba/tools/readgroup.yml#readgroup_fastq_pe_uuid[] | ||
| readgroup_fastq_se_uuid_list | https://w3id.org/cwl/view/git/3fa737f9162bbfbdbc243a3b1ff7c8e110875eba/tools/readgroup.yml#readgroup_fastq_se_uuid[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| load_bai |
../../tools/bio_client_upload_pull_uuid.cwl
(CommandLineTool)
|
||
| load_bam |
../../tools/bio_client_upload_pull_uuid.cwl
(CommandLineTool)
|
||
| transform |
transform.cwl
(Workflow)
|
||
| load_sqlite |
../../tools/bio_client_upload_pull_uuid.cwl
(CommandLineTool)
|
||
| emit_bai_uuid |
../../tools/emit_json_value.cwl
(ExpressionTool)
|
||
| emit_bam_uuid |
../../tools/emit_json_value.cwl
(ExpressionTool)
|
||
| emit_sqlite_uuid |
../../tools/emit_json_value.cwl
(ExpressionTool)
|
||
| root_fasta_files |
../../tools/root_fasta_dnaseq.cwl
(CommandLineTool)
|
||
| extract_known_snp |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_capture_kits |
extract_capture_kit.cwl
(Workflow)
|
||
| extract_reference_fa |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_reference_sa |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| root_known_snp_files |
../../tools/root_vcf.cwl
(CommandLineTool)
|
||
| extract_amplicon_kits |
extract_amplicon_kit.cwl
(Workflow)
|
||
| extract_reference_amb |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_reference_ann |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_reference_bwt |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_reference_fai |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_reference_pac |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_readgroups_bam |
extract_readgroups_bam.cwl
(Workflow)
|
||
| extract_reference_dict |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_known_snp_index |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_readgroup_fastq_pe |
extract_readgroup_fastq_pe.cwl
(Workflow)
|
||
| extract_readgroup_fastq_se |
extract_readgroup_fastq_se.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| indexd_bai_uuid | String | ||
| indexd_bam_uuid | String | ||
| indexd_sqlite_uuid | String |
Permalink:
https://w3id.org/cwl/view/git/3fa737f9162bbfbdbc243a3b1ff7c8e110875eba/workflows/bamfastq_align/etl.cwl
