Workflow: dropEst pipeline
Fetched 2025-04-23 21:59:25 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| threads | Integer | Number of threads for STAR aligner | |
| fastq_r1 | File | R1 FASTQ file | |
| fastq_r2 | File | FASTQ file 2 |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| star |
steps/star.cwl
(CommandLineTool)
|
STAR aligner, 2.6.1e with GRCh38 index | |
| dropest |
steps/dropest.cwl
(CommandLineTool)
|
dropEst pipeline, v0.8.6 | |
| droptag |
steps/droptag.cwl
(CommandLineTool)
|
droptag | |
| concat_fastq_gz |
steps/concat-fastq-gz.cwl
(CommandLineTool)
|
Concatenate dropEst .fastq.gz files |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam_file | File | Aligned reads | |
| mtx_output | File | Count matrix in .mtx format | |
| rds_output | File | Output in RDS format | |
| tsv_output | File[] | Gene/cell metadata |
Permalink:
https://w3id.org/cwl/view/git/ea70d9d497245a1d5da7c4b692f8da93d364b10a/dropest.cwl
