Workflow: bulk scRNA-seq pipeline using Salmon

Fetched 2024-12-04 08:26:39 GMT
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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