Workflow: etl.cwl
Fetched 2023-01-12 12:04:43 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 | ||
| start_token | File | ||
| thread_count | Long | ||
| bioclient_config | File | ||
| 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 | ||
| 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 | ||
| reference_dict_file_size | Long | ||
| known_snp_index_file_size | Long |
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_mirna.cwl
(Workflow)
|
||
| extract_bam |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| load_sqlite |
../../tools/bio_client_upload_pull_uuid.cwl
(CommandLineTool)
|
||
| extract_ref_fa |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_ref_sa |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| generate_token |
../../tools/generate_load_token.cwl
(CommandLineTool)
|
||
| extract_ref_amb |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_ref_ann |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_ref_bwt |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_ref_fai |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_ref_pac |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_ref_dict |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| root_fasta_files |
../../tools/root_fasta_dnaseq.cwl
(CommandLineTool)
|
||
| extract_known_snp |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| rename_mirnas_quant |
../../tools/rename.cwl
(CommandLineTool)
|
||
| tar_mirna_profiling |
../../tools/tar.cwl
(CommandLineTool)
|
||
| root_known_snp_files |
../../tools/root_vcf.cwl
(CommandLineTool)
|
||
| rename_isoforms_quant |
../../tools/rename.cwl
(CommandLineTool)
|
||
| extract_known_snp_index |
../../tools/bio_client_download.cwl
(CommandLineTool)
|
||
| load_tar_mirna_profiling |
../../tools/bio_client_upload_pull_uuid.cwl
(CommandLineTool)
|
||
| tar_mirna_profiling_graph_libs |
../../tools/tar_dir.cwl
(CommandLineTool)
|
||
| load_mirna_profiling_mirnas_quant |
../../tools/bio_client_upload_pull_uuid.cwl
(CommandLineTool)
|
||
| load_mirna_profiling_isoforms_quant |
../../tools/bio_client_upload_pull_uuid.cwl
(CommandLineTool)
|
||
| tar_mirna_profiling_alignment_stats |
../../tools/tar_dir.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| token | File | ||
| indexd_bai_json | File | ||
| indexd_bam_json | File | ||
| indexd_sqlite_json | File | ||
| indexd_mirna_profiling_tar_json | File | ||
| indexd_mirna_profiling_mirnas_quant_json | File | ||
| indexd_mirna_profiling_isoforms_quant_json | File |
Permalink:
https://w3id.org/cwl/view/git/d6c0acb0a5e8546dc96463c9d184ca96548e22b3/workflows/mirnaseq/etl.cwl
