Workflow: bulk scRNA-seq pipeline using Salmon
Fetched 2025-09-05 20:31:47 GMT
Verified with cwltool version 3.1.20230201224320
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- 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 |
|---|---|---|---|
| threads | Integer | Number of threads for Salmon | |
| fastq_dir | Directory | Directory containing FASTQ files |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastqc |
steps/fastqc.cwl
(CommandLineTool)
|
Runs fastQC on each fastq file in fastq directory | |
| salmon-bulk |
steps/bulk-salmon.cwl
(CommandLineTool)
|
Run Salmon quant tool on FASTQ input | |
| make_expression_matrix |
steps/expression-matrix.cwl
(CommandLineTool)
|
Takes gene expression vectors from several bulk RNA samples and makes them into a gene by sample matrix |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fastqc_dir | Directory | Directory of FastQC output files, mirroring input directory structure | |
| salmon_output | Directory | Full output of `salmon quant` | |
| expression_matrix | File | A hd5 file containing transcript by sample matrices of TPM and number of reads |
Permalink:
https://w3id.org/cwl/view/git/d18fd4992c69eadfad82186d1e16a07092477552/bulk-pipeline.cwl
