I have a tool that utilizes a singularity container, however, I am on an HPC where the singularity module must be loaded prior to using a container. The command for this is “module load singularity”.
I’m trying to load the singularity module before running my command but the below code gives me an “Expression evaluation error”.
What am I doing wrong? Is there a better way to do this?
class: CommandLineTool
cwlVersion: v1.2
requirements:
- class: InlineJavascriptRequirement
baseCommand: [ "bash", "-c" ]
inputs:
in_gff:
type: File
singularity_image:
type: string
arguments:
- valueFrom: |
module load singularity &&
singularity exec ${inputs.singularity_image} flatfile-to-json.pl --gff ${inputs.in_gff} --tracklabel 1 --out data/
outputs:
out_trackList:
type: File
outputBinding:
glob: data/trackList.json
out_tracks:
type: Directory
outputBinding:
glob: data/tracks