Workflow: exomeseq-gatk4-03-organizedirectories.cwl
Fetched 2026-10-25 14:42:07 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 | 4e800cdbdf4a40ac308ebd6b845b5460[] | ||
| fastqc_reports | f20ca1810d6a12f72dfe85a60b69b111[] | ||
| bams_recalibrated | File[] | ||
| bams_markduplicates | File[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| org_raw_variants |
../tools/files-to-directory.cwl
(ExpressionTool)
|
Moves an array of Files into a named directory | |
| org_trim_reports |
../tools/file-pairs-to-directory.cwl
(ExpressionTool)
|
Moves an array of File pairs into a named directory | |
| org_fastqc_reports |
../tools/file-pairs-to-directory.cwl
(ExpressionTool)
|
Moves an array of File pairs into a named directory | |
| org_bams_recalibrated |
../tools/files-to-directory.cwl
(ExpressionTool)
|
Moves an array of Files into a named directory | |
| org_bams_markduplicates |
../tools/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 |
Permalink:
https://w3id.org/cwl/view/git/92b8d41bab2661919aa11aa84e1923748f8503c4/subworkflows/exomeseq-gatk4-03-organizedirectories.cwl
