/
bulk-pipeline.cwl
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bulk-pipeline.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0
label: bulk scRNA-seq pipeline using Salmon
#requirements:
# ScatterFeatureRequirement: {}
# SubworkflowFeatureRequirement: {}
inputs:
fastq_dir:
label: "Directory containing FASTQ files"
type: Directory
threads:
label: "Number of threads for Salmon"
type: int
default: 1
outputs:
fastqc_dir:
outputSource: fastqc/fastqc_dir
type: Directory
label: "Directory of FastQC output files, mirroring input directory structure"
salmon_output:
outputSource: salmon-bulk/output_dir
type: Directory
label: "Full output of `salmon quant`"
expression_matrix:
outputSource: make_expression_matrix/expression_matrix
type: File
label: "A hd5 file containing transcript by sample matrices of TPM and number of reads"
steps:
- id: fastqc
in:
- id: fastq_dir
source: fastq_dir
- id: threads
source: threads
out:
- fastqc_dir
run: steps/fastqc.cwl
label: "Run fastqc on all fastq files in fastq directory"
- id: salmon-bulk
in:
- id: fastq_dir
source: fastq_dir
- id: threads
source: threads
out:
- output_dir
run: steps/bulk-salmon.cwl
label: "Salmon quant 1.0.0, with index from GRCh38 transcriptome"
- id: make_expression_matrix
in:
- id: quant_dir
source: salmon-bulk/output_dir
out:
- expression_matrix
run: steps/expression-matrix.cwl
label: "Make expression matrix from quant vectors"