Arvados

Bug #9674

Updated by Bryan Cosca over 7 years ago

<pre> 
 #!/usr/bin/env cwl-runner 
 cwlVersion: v1.0 
 class: CommandLineTool 
 baseCommand: [] 
 requirements: 
   InlineJavascriptRequirement: {} 
   InitialWorkDirRequirement: 
     listing: 
       - $(inputs.inputsam) 
 inputs: 
   splitSamIntoChrom: 
     type: File 
     inputBinding: 
       position: 0 
   chr-chrom-lst: 
     type: File 
     inputBinding: 
       position: 1 
   inputsam: 
     type: File 
     inputBinding: 
       position: 2 
       valueFrom: $(self.basename) 
 outputs: 
   output-sam: 
     type: 
       type: array 
       items: File 
     outputBinding: 
       glob: "*sam" 
 </pre> 

 <pre> 
 


 arvados-cwl-runner --local splitsam-test.cwl splitsam-test.json  
 /usr/local/bin/arvados-cwl-runner 1.0.20160713211920, arvados-python-client 0.1.20160713191718, cwltool 1.0.20160712154127 
 2016-07-27 19:11:13 arvados.cwl-runner[64747] INFO: Pipeline instance qr1hi-d1hrv-2fb0mcilpm2ehpf 
 2016-07-27 19:11:14 arvados.arv-run[64747] INFO: Upload local files: "splitSamIntoChrom.pl" "chr_chrom.lst" 
 2016-07-27 19:11:14 arvados.arv-run[64747] INFO: Using collection qr1hi-4zz18-gow6notm9tzd0wa 
 2016-07-27 19:11:20 arvados.cwl-runner[64747] ERROR: Caught unhandled exception, marking pipeline as failed.    Error was: [Errno 2] No such file or directory: '$(task.outdir)/keep:c00bea363a0770335e81662bb7980051+269668/sample.sam' 
 Workflow error, try again with --debug for more information: 
   Workflow did not return a result. 
 </pre> 

 <pre> 
 


 { 
   "splitSamIntoChrom":{ 
         "class":"File", 
         "path":"splitSamIntoChrom.pl" 
   }, 
   "chr-chrom-lst":{ 
         "class":"File", 
         "path":"chr_chrom.lst" 
   }, 
   "inputsam":{ 
         "class":"File", 
         "path":"keep:c00bea363a0770335e81662bb7980051+269668/sample.sam" 
   } 
 } 
 </pre>

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