Bug #13849

Updated by Jiayong Li over 3 years ago

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.
<pre>
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"
}
</pre>

This means the secondaryFiles checks failed in the single container version. See the attached tar ball for cwl. Run with
<pre>
arvados-cwl-runner phasing-wf.cwl phasing-NA12878.yml
</pre>

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