combine outputs

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  • Beri Shifaw

    Hi Sehyun Oh

    What task is failing and what is the error message? It would be helpful if you could attach the stdout and stderr log files. 

     

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  • Sehyun Oh

    Hi Beri,

    There is no error - everything runs 'successfully'. But the outputs from SelectVariants never be used as a list of input files (= multiple -V arguments) for CombineVariants. So each sample gives its own output from CombineVariants... without combining... ;(

    Let me know if you need any other information to understand/solve this issue. 

    - Sehyun

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  • Beri Shifaw

    That's odd, your WDL look fine at first sight. Mind sharing the workspace you're running this workflow in with GROUP_FireCloud-Support@firecloud.org so that we can view the standard log files? 

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  • Sehyun Oh

    Ok. I just added the email as a reader of my workspace (TOSC19-CNVWorkflow_master). Below are the submission ids for jobs with or without CreateFoFN.

    Tool with CreateFoFN >>> submission-id: 4ffed12b-3186-4516-b1c4-cd96baba90cf (paused)

    Tool without CreateFoFN >>> submission-id: f4f096fb-7b57-4671-af75-29387e14f05b

     

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  • Beri Shifaw

    Lets try running the workflow without the "CreateFoFN" again but instead of running the workflow on the Sample, select  Sample_set from the drop down menu in the Tool configurations.

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  • Sehyun Oh

    Ok. I just submitted the job with a sample_set of 3 samples, without CreateFoFN.

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  • Beri Shifaw

    After setting the Tool config to sample_set you'll still need to click on "Select Data" and select the sample set you would like to process. Try   `MuTect1_PON_2019-06-26T03-05-56`

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  • Sehyun Oh

    I clicked 'Select Data' button and selected a set with three samples (MuTect1_PON_2019-06-18T01-13-55), which failed (submission ID: 4ffa7acc-b649-4268-bed6-407df436a). I started a job again with `MuTect1_PON_2019-06-26T03-05-56` dataset. Btw, since last night, my job requests repeatedly stuck at 'submitted' step... fyi.

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  • Beri Shifaw

    Thanks for the info, I've notified the dev team and they working towards resolving the job manager issue. 

    For your Tool configuration you'll need to edit the input attributes for "normal_bams" and "normal_bais" so that they work with sample_sets.  This means adding "samples" in your argument before adding the column name. Use the following parameters: 

    normal_bams : this.samples.synthExomeBam

    normal_bais : this.samples.synthExomeBamIndex

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  • Beri Shifaw

    Looks like your workflow completed and with a single pon VCF. Are you all set? 

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  • Sehyun Oh

    Yeah! Thanks a lot for your help, Beri! 

    Just one more question, how can I explain "why I should use 'sample_set' instead of 'sample'" for CombineVariants? Why scatter is not enough? 

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  • Beri Shifaw

    It's not related to the CombineVariants task but to your workflow as a whole. Your workflow is expecting and array of files as input but when you select Samples as the "root entity" your telling Terra to pass one input file at a time to your workflow. So your workflow was given 1 sample bam to process. You were also selecting more than 1 sample while your root entity was set to Sample mode which tells Terra run this workflow once for each of the samples you've have selected. 

    On the other hand if you wanted to run a workflow flow once and pass this workflow an array of sample files (e.g. Bam files) then you would choose sample_set for your root entity. 

      

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  • Sehyun Oh

    Got it. Thanks!!

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