switch docker

workflows/deseq2/Dockerfile

+FROM quay.io/biocontainers/bioconductor-deseq2:1.42.0--r43hf17093f_2
+
+# Since our base image is an R docker base we will use BiocManager install
+
+RUN apt-get update && \ 
+    R -e "install.packages(c('BiocManager'), repos='https://cloud.r-project.org/');BiocManager::install('tximport')" && \
+    apt-get clean -y
\ No newline at end of file

workflows/deseq2/deseq2-localDocker-test.cwl

+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+  DockerRequirement:
+    dockerFile: {$include: "./Dockerfile"}
+    dockerImageId: "deseq-docker"
+requirements:
+  - class: NetworkAccess
+    networkAccess: true
+baseCommand: [Rscript, --help]
+
+inputs: []
+
+outputs: []

workflows/deseq2/deseq2.cwl

+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.2
 class: CommandLineTool
-# hints:
-#   DockerRequirement:
-#     dockerPull: r-base:4.4.2
+hints:
+  # DockerRequirement:
+  #   dockerPull: quay.io/biocontainers/bioconductor-deseq2:1.42.0--r43hf17093f_2
+  DockerRequirement:
+    dockerFile: {$include: "./Dockerfile"}
+    dockerImageId: "deseq-docker"
 requirements:
   - class: InitialWorkDirRequirement
     listing:
@@ -11,7 +16,7 @@ requirements:
           $include: deseq2.R
   - class: NetworkAccess
     networkAccess: true
-baseCommand: [RScript, deseq2.R]
+baseCommand: [Rscript, deseq2.R]
 inputs:
   inKallistoResults:
     type: Directory

workflows/deseq2/r-docker-test.cwl

+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.2
 class: CommandLineTool
 
 requirements:
-  - class: NetworkAccess
-    networkAccess: true
-  # - class: DockerRequirement
-  #   dockerPull: r-base:4.4.2
+  - class: DockerRequirement
+    dockerPull: quay.io/biocontainers/bioconductor-deseq2:1.42.0--r43hf17093f_2
 
-baseCommand: [RScript, --help]
+baseCommand: [Rscript, --help]
 
 inputs: []
-  
+
 outputs: []
-  
\ No newline at end of file