rm dockerfile sleuth

workflows/sleuth/Dockerfile

-# Use an official R base image
-FROM rocker/r-ver:4.1.3
-
-# Install system dependencies for R packages and other utilities
-RUN apt-get update && apt-get install -y \
-    libcurl4-openssl-dev \
-    libssl-dev \
-    libxml2-dev \
-    git \
-    build-essential \
-    && rm -rf /var/lib/apt/lists/*
-
-# Install BiocManager
-RUN R -e "install.packages('BiocManager')"
-
-# Install Bioconductor version 3.14
-RUN R -e "BiocManager::install(version = '3.11')"
-
-# Install sleuth from Bioconductor
-RUN R -e "BiocManager::install('sleuth')"
-
-# Install other necessary CRAN packages
-RUN R -e "install.packages('jsonlite', repos='https://cran.r-project.org')"
-
-# Set the working directory to /app
-WORKDIR /app
-
-# Default command to run when the container starts
-CMD ["R"]

workflows/sleuth/workflow.cwl

@@ -4,9 +4,6 @@ cwlVersion: v1.2
 class: CommandLineTool
 
 hints:
-  # DockerRequirement:
-  #   dockerImageId: "sleuth"
-  #   dockerFile: {$include: "Dockerfile"}
   DockerRequirement: 
     dockerPull: quay.io/biocontainers/mulled-v2-fdd016122f200fdc6dc30f6ea2fd0000e8067dff:f9531f6ac1f44332eff70b5912d7d5f3ebe8df38-0