- 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 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/536d6ed4bc639b93a8d8bc1c1a694b848d4d6f32/bulk-pipeline.cwl