Workflow: exomeseq-gatk4-03-organizedirectories.cwl
Fetched 2025-02-26 14:37:16 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:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| raw_variants | File[] | ||
| trim_reports | 0da823559fab44e0ede2d96357040754[] | ||
| fastqc_reports | a2decf6d0d4ea8abe628df48b5e725d7[] | ||
| bams_recalibrated | File[] | ||
| bams_markduplicates | File[] | ||
| metrics_markduplicates | File[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| org_raw_variants |
../utils/files-to-directory.cwl
(ExpressionTool)
|
Moves an array of Files into a named directory | |
| org_trim_reports |
../utils/file-pairs-to-directory.cwl
(ExpressionTool)
|
Moves an array of File pairs into a named directory | |
| org_fastqc_reports |
../utils/file-pairs-to-directory.cwl
(ExpressionTool)
|
Moves an array of File pairs into a named directory | |
| org_bams_recalibrated |
../utils/files-to-directory.cwl
(ExpressionTool)
|
Moves an array of Files into a named directory | |
| org_bams_markduplicates |
../utils/files-to-directory.cwl
(ExpressionTool)
|
Moves an array of Files into a named directory | |
| org_metrics_markduplicates |
../utils/files-to-directory.cwl
(ExpressionTool)
|
Moves an array of Files into a named directory |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| raw_variants_dir | Directory | ||
| trim_reports_dir | Directory | ||
| fastqc_reports_dir | Directory | ||
| bams_recalibrated_dir | Directory | ||
| bams_markduplicates_dir | Directory | ||
| metrics_markduplicates_dir | Directory |
Permalink:
https://w3id.org/cwl/view/git/5438ab97697f9a9b246719302bedc79f305a98f5/subworkflows/exomeseq-gatk4-03-organizedirectories.cwl
