Workflow: star_samtools_stringtie_prepDE_DESeq2.cwl
Fetched 2026-07-18 09:39:06 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:
GNU General Public License v3.0 only
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq1 | File[] | ||
| fastq2 | File[] | ||
| fastq3 | File[] | ||
| fastq4 | File[] | ||
| threads | Integer | ||
| metadata | File | ||
| genomeDir | Directory | ||
| annotation | File | ||
| DESeq2_script | File | ||
| prepDE_script | File | ||
| subject_name1 | String | ||
| subject_name2 | String | ||
| subject_name3 | String | ||
| subject_name4 | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| DESeq2 |
../tools/DESeq2.cwl
(CommandLineTool)
|
||
| prepDE |
../tools/prepDE.cwl
(CommandLineTool)
|
||
| samtools_1 |
../tools/samtools.cwl
(CommandLineTool)
|
||
| samtools_2 |
../tools/samtools.cwl
(CommandLineTool)
|
||
| samtools_3 |
../tools/samtools.cwl
(CommandLineTool)
|
||
| samtools_4 |
../tools/samtools.cwl
(CommandLineTool)
|
||
| star_folder |
../tools/folder.cwl
(ExpressionTool)
|
||
| stringtie_1 |
../tools/stringtie.cwl
(CommandLineTool)
|
||
| stringtie_2 |
../tools/stringtie.cwl
(CommandLineTool)
|
||
| stringtie_3 |
../tools/stringtie.cwl
(CommandLineTool)
|
||
| stringtie_4 |
../tools/stringtie.cwl
(CommandLineTool)
|
||
| DESeq2_folder |
../tools/folder.cwl
(ExpressionTool)
|
||
| prepDE_folder |
../tools/folder.cwl
(ExpressionTool)
|
||
| star_readmap_1 |
../tools/STAR_readmap.cwl
(CommandLineTool)
|
||
| star_readmap_2 |
../tools/STAR_readmap.cwl
(CommandLineTool)
|
||
| star_readmap_3 |
../tools/STAR_readmap.cwl
(CommandLineTool)
|
||
| star_readmap_4 |
../tools/STAR_readmap.cwl
(CommandLineTool)
|
||
| samtools_folder |
../tools/folder.cwl
(ExpressionTool)
|
||
| stringtie_folder |
../tools/folder.cwl
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| DESeq2_out | Directory | ||
| prepDE_out | Directory | ||
| samtools_out | Directory | ||
| stringtie_out | Directory | ||
| star_readmap_out | Directory |
Permalink:
https://w3id.org/cwl/view/git/54adf7fcfbf48c9cc4cfcf384e04eede39b5e5f6/workflows/star_samtools_stringtie_prepDE_DESeq2.cwl
