We've moved!
You can find our new documentation site and support forum for posting questions here.

cannot run "CGA_WES_Characterization_Pipeline_v0.1_Dec2018" pipeline for paired tumor analysis

I try to run the "CGA_WES_Characterization_Pipeline_v0.1_Dec2018" pipeline for paired tumor analysis on Firecloud.
A common error that I get is “expected single value for workflow input, but evaluated result set was empty”. I modify the workflow inputs, but I get error again. I would greatly appreciate your advice. Thank you!

Answers

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @kribio I will take a look at this and get back to you shortly!

  • birgerbirger Member, Broadie, CGA-mod ✭✭✭

    Did you create your workspace by cloning either of the two template workspaces? If you share your workspace with me ([email protected]) I can take a closer look at the error message and track down its source. Please post this to the Cancer Genome Analysis category in the FireCloud form; I'd prefer responding there.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @kribio Additionally, there is a discussion here that describes a potential solution to this error. It is to make sure that your attributes in your Data Model are the same case as listed in the Method Configuration.

  • kribiokribio Member
    edited January 2019

    @[email protected].org yes, I cloned the template workspace. This is the path with the workspace and the method cofiguration: https://portal.firecloud.org/#workspaces/pecomabwh1/Kwiatkowski_PeComa_Cohort_10-18/method-configs/getzlab/CGA_WES_Characterization_Pipeline_v0.1_Dec2018

    And here the errors I get:
    GA_Production_Analysis_Workflow.readGroupBlackList - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.ContEST_Task.HapMapVCF - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.tumorBamIdx - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.DB_SNP_VCF_IDX - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.CopyNumberReportQC_Task.captureNormalsDBRCLZip - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.refFastaIdx - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.refFasta - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.CopyNumberReportQC_Task.regionFile - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.gatk_acnv_only.common_snp_list - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.normalBam - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.cosmicVCF - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.DB_SNP_VCF - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.gatk_acnv_only.PoN - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.cytoBandFile - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.ContEST_Task.SNP6Bed - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.GATK4_JAR - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.MutectFC_Task.mutectIntervals - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.tumorBam - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.GatherAndDeTiN_Task.exac_pickle - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.normalBamIdx - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.baitIntervals - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.refFastaDict - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.blat.hg19_bit - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.VEP_Task.VEP_File - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.cga_pipeline_config - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.PONs_list - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.Oncotate_Task.oncoDBTarBall - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.CrossCheckLaneFingerprints_Task.HaplotypeDBForCrossCheck - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.Strelka.config - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.MuTectNormalPanel - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.gatk_acnv_only.gatk_protected - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.targetIntervals - Expected single value for workflow input, but evaluated result set was empty
    CGA_Production_Analysis_Workflow.lego_plotter_task.mut_categs - Expected single value for workflow input, but evaluated result set was empty
    n/a

    What is wrong? Thank you in advance!

  • birgerbirger Member, Broadie, CGA-mod ✭✭✭

    @kribio , could you give me read access to your workspace so I can go into it and look at your method config. My firecloud userid is just my broad email: [email protected]

    I'm guessing your method config is not correctly referencing all of the workflow's default reference files and config files. There is either a problem with the workspace attribute definitions or the method config.

  • kribiokribio Member

    @ [email protected] I provided you access as a writer so you can modify it. Thank you very much!

  • birgerbirger Member, Broadie, CGA-mod ✭✭✭

    @kribio, you did not clone the correct template workspace, and as a result you do not have the appropriate workspace attributes defined. Please read the How to Use this Workflow section of the user guide. It points you to the correct template workspace and explains the changes you will need to make to your clone.

  • kribiokribio Member

    @ [email protected] I cloned the template workspace " broad-fc-getzlab-workflows/CGA_WES_Characterization_OpenAccess". Thank you for the updated guidelines. I will consider it and make the appropriate changes on my workspace.

Sign In or Register to comment.