#!/usr/bin/env cwl-runner doc: | DESeq2 example workflow This workflow runs DESeq2 on the output of the kallisto workflow and the metadata file. It runs an R script, deseq2.R, which ideally should be split into three sub scripts and accordingly three workflow steps 1. Read kallsito data 2. Prep / run deseq2 3. Plot results cwlVersion: v1.2 class: CommandLineTool hints: DockerRequirement: dockerPull: quay.io/biocontainers/mulled-v2-05fd88b9ac812a9149da2f2d881d62f01cc49835:a10f0e3a7a70fc45494f8781d33901086d2214d0-0 requirements: - class: InitialWorkDirRequirement listing: - entryname: deseq2.R entry: $include: deseq2.R - class: NetworkAccess networkAccess: true baseCommand: [Rscript, deseq2.R] inputs: inKallistoResults: type: Directory inputBinding: position: 1 inMetadataFile: type: File inputBinding: position: 2 inMetadataSample: type: string inputBinding: position: 3 inMetadataFactorList: type: string[] inputBinding: position: 4 outputs: output: type: File[] outputBinding: glob: - "*.svg" - "*.csv"