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Why does this work on command line but not when executed via cromwell?

Hello,
I have the following commands wrapped in a WDL task:

        source /broad/software/scripts/useuse
        use BWA
        use Samtools
        bwa mem -t 8 -R ${read_group} ${ref} ${fq1} ${fq2} | samtools view -bS - > ${sample_name}.aligned.bam

The above is trying to generate an aligned BAM without the hard-disk overhead of an intermediary SAM file. It works when I do it manually on command line. However, when executed as part of a WDL, I get a truncated BAM that's only 93 bytes in size.The stderr doesn't show anything informative except I noticed that BWA reports a shorter CPU time than when I do it manually, which makes sense.

Any clue as to what might be happening or alternate ways to do this?

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Answers

  • mcovarrmcovarr Cambridge, MAMember, Broadie, Dev

    Could you peek inside the appropriate script file in the job's execution directory to see if the bwa command that was written looks like what you expect?

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