Workflow: hisat2_htseq_dexseq.cwl
Fetched 2023-01-12 16:37:20 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 | ||
| dexseq_script | File | ||
| subject_name1 | String | ||
| subject_name2 | String | ||
| subject_name3 | String | ||
| subject_name4 | String | ||
| htseq_count_script | File | ||
| htseq_prepare_script | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| dexseq |
../tools/dexseq.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)
|
||
| dexseq_folder |
../tools/folder.cwl
(ExpressionTool)
|
||
| htseq_count_1 |
../tools/htseq_count.cwl
(CommandLineTool)
|
||
| htseq_count_2 |
../tools/htseq_count.cwl
(CommandLineTool)
|
||
| htseq_count_3 |
../tools/htseq_count.cwl
(CommandLineTool)
|
||
| htseq_count_4 |
../tools/htseq_count.cwl
(CommandLineTool)
|
||
| htseq_prepare |
../tools/htseq_prepare.cwl
(CommandLineTool)
|
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| hisat2_align_1 |
../tools/hisat2_align.cwl
(CommandLineTool)
|
||
| hisat2_align_2 |
../tools/hisat2_align.cwl
(CommandLineTool)
|
||
| hisat2_align_3 |
../tools/hisat2_align.cwl
(CommandLineTool)
|
||
| hisat2_align_4 |
../tools/hisat2_align.cwl
(CommandLineTool)
|
||
| samtools_folder |
../tools/folder.cwl
(ExpressionTool)
|
||
| htseq_count_folder |
../tools/folder.cwl
(ExpressionTool)
|
||
| hisat2_align_folder |
../tools/folder.cwl
(ExpressionTool)
|
||
| htseq_prepare_folder |
../tools/folder.cwl
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| dexseq_out | Directory | ||
| samtools_out | Directory | ||
| htseq_count_out | Directory | ||
| hisat2_align_out | Directory | ||
| htseq_prepare_out | Directory |
Permalink:
https://w3id.org/cwl/view/git/bbbbd9dd412a6abfee9bb0c9e9754cb8b5294b02/workflows/hisat2_htseq_dexseq.cwl
