broadinstitute/wdltool

Error message for incorrect output string

Closed this issue · 1 comments

meganshand commented

The following task results in an uninformative error message when using validate:

task printReads {
    File bam
    File ref_fasta
    File ref_fasta_index
    File ref_dict

    command {
        java -jar /usr/gitc/GenomeAnalysisTK.jar \
        -T PrintReads \
        -I ${bam} \
        -o smaller.bam \
        -L chr1 \
        -R ${ref_fasta}
    }
    runtime {
        docker: "broadinstitute/genomes-in-the-cloud:1.1010_with_gatk3.5"
        disks: "local-disk 400 SSD"
        memory: "10 GB"
    }
    output {
        File smaller = smaller.bam
    }
}

results in this error message:

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

The problem is that there aren't quotes around "smaller.bam" in the outputs of the task. It would be great if the error message could tell you which line or object was causing the problem. The error message from cromwell is different, but also uninformative and it would be great if the error message could be clearer there as well.