Arvados

single container
https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-1vziek0s8udmajx

non-single container
https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-g0u996tfq07d4mp

Note that the non-single container run failed, with the secondaryFiles checks prompted errors, as they should.

cwltool ERROR: Cannot make scatter job: Missing required secondary file 'chr1.1kg.phase3.v5a.vcf.gz.tbi' from file object: {
    "basename": "chr1.1kg.phase3.v5a.vcf.gz", 
    "nameroot": "chr1.1kg.phase3.v5a.vcf", 
    "nameext": ".gz", 
    "location": "keep:ba7cd392bc4aa229c3c771b496e79628+9990/chr1.1kg.phase3.v5a.vcf.gz", 
    "secondaryFiles": [], 
    "class": "File" 
}

This means the secondaryFiles checks failed in the single container version. See the attached tar ball for cwl. Run with

arvados-cwl-runner phasing-wf.cwl phasing-NA12878.yml