Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.

Incremental files between wdl-calls


inspired by a post from @Vzzarr https://gatkforums.broadinstitute.org/gatk/discussion/10529/how-to-run-the-entire-pipeline-using-even-spark-tools-from-java#latest I would like to ask if it would be possible to write only the changes (deltas) to a file as an output (like the way common backup-solutions do)? The aim is to reduce time/space/operations for writing the intermediate files during a wdl-workflow.

As an example think of the pre-processing part of the pipeline, which creating several bam-files, but every bam-files changes only a bit in every step, seen by the level of information.

Greetings EADG


Best Answer


  • EADGEADG KielMember ✭✭✭

    Hi @kshakir,

    thanx for the answer I will try out the NIO-features.

    Sry for the late response...but the notifications section isn't working for me probably since the update of the forum.

    Greetings EADG

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