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CHANGELOG.md

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1.0.7

  • incrementing the Delly Docker container from 1.3 to 1.4 to address multi-tumor file upload prep problem

1.0.6

  • Fixed a bug which caused *somatic.indel.vcf.gz.tbi to be added twice.
  • Added a Docker file which can be used to build an image containing this workflow.

1.0.5

  • the plotting code for the DKFZ container now uses <60G RAM (DKFZ 1.3 image)
  • correctly combine the timing and QC json files, so it now supports the merged upload but also multi-tumor statistics collection
  • combined upload, now using a single upload for DKFZ and EMBL sub-workflows, the official name is EMBLDKFZPancancerStrCnIndelSNV
  • fixed a bug where upload server was used for the metadata URLs, actually needed to be download server

1.0.4

  • incrementing the version of the delly Docker image to 1.1, this image only changes the base Docker image used to build, it makes no scientific changes

1.0.3

  • includes a bug fix for offline mode where XML file paths were not set correctly.

1.0.2

  • re-orders upload to occur after both workflows are ready
  • fixes default ini file paths
  • fixes issue with pem key for gnos mounted in wrong location (fails workflows when running the first time without reference data handy)
  • reverts the version change for dkfz which is hardcoded in Roddy (fails workflow across the board)

1.0.1

Version 1.0.1 represents non-scientific changes and mostly focus on the usability of local file mode, result archiving, and running workflows as non-root inside containers

  • bug fixes to support creation of upload archive
  • getting full offline mode working, ability to supply XML metadata files was the largest change
  • run workflows as a non-root user
  • docs updated

1.0.0

  • Initial release
  • Do not schedule 1.0.0 with multiple-tumor donors!! 1.0.1 will support this

TODO

  • on first run, the workflow pulls reference files from S3 and GNOS, we need a better alternative so that we do not eventually refer to broken links which would decrease the longevity of the workflow
  • artifact for shared workflow modules that we can use for Sanger, DKFZ, EMBL, and maybe BWA workflows... specifically modules for upload download
  • need to switch to --uuid for uploader so I know the output archive file name
  • I may want to rethink the upload options so that you can upload to both S3 and GNOS at the same time, for example
  • DKFZ is missing timing JSON file, I co-opted this for my full-workflow timing metrics but we really should get them to supply this and just add to it. Also EMBL timing metrics need a total wall-time.
  • print some helpful messages before the workflow runs indicating where the output will be, touch files for completion, what modes have been set, etc