Arvados

Bug #13849

Updated by Jiayong Li almost 6 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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