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Remove intermediary files of workflow to prevent storage flood

In a typical SNV/INDEL identification workflow, fastq files are serially converted to bam, sorted-bam, marked-duplicates.bam, base-quals-recalibrated.bam which floods my limited storage space, especially when I process many samples. What is the best practice to remove intermediary big files? Add a rm inputBam at the end of the command-block of a task-block?

Best Answer


  • Irsan_KooiIrsan_Kooi Member
    edited December 2016

    OK, we are working on an EC2 instance at AWS, I will just increase the storage volume then. Thanks for you help!

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