Singularity?

[R-Cardenas]

Hi, is there any advice for running using sinuglarity?

I tried using a newer version of CWL (2.0.20200128065236) than the reccomended. And when running cwltool quay.io/pancancer/pcawg-dkfz-workflow:2.2.0 Dockstore.json even without the singularity flag, I get the following error:

Workflow error, try again with --debug for more information:
Missing required secondary file 'normal_sample.bam.bai' from file object: {
"class": "File",
"location": "file:///Users/aft19qdu/Documents/singularity/DKFZ/bams/normal_sample.bam",
"basename": "normal_sample.bam",
"nameroot": "normal_sample",
"nameext": ".bam",
"secondaryFiles": []
}

I hope you can help!
Best
Ryan