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.