Workflow: bulk scRNA-seq pipeline using Salmon
Fetched 2023-05-10 17:37:26 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
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- Inputs/Outputs
Unknown workflow license, check
source repository.
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 |
|---|---|---|---|
| quant_files | File[] | Files containing transcript expression data from salmon quant | |
| command_info | File[] | Log of command parameters supplied to salmon quant | |
| report_files | File[] | HTML reports with embedded graphs | |
| zipped_files | File[] | Individual graph files and additional data files containing the raw data from which plots were drawn. | |
| auxiliary_files | File[] | Tarred and zipped directory containing miscellaneous auxiliary files produced by 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/c01ba083d8467df40f3b87a86712a3965111d90e/bulk-pipeline.cwl
