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June 01, 2020

Derek Caetano-Anolles

The following release notes correspond to May 22, 2020 - June 1, 2020. In addition to these changes, this release includes back-end updates to workflows, Google integrations, and notebooks to improve upcoming features.

User Interface

  • Running jobs against multiple sample sets in a single submission is now allowed. This effectively removes the limit of processing 10 sets at a time by bundling them into a single submission, instead of creating parallel submissions. (Note that TSV functions in the Data tab does not currently work for sets of sets.)

Notebooks

  • Notebooks can now handle user emails with non-standard characters in them, such as % signs.
  • Notebooks now include the newest versions of R (v4.0) and Bioconductor (v3.11.0). The following environments have been added:
    • Default: GATK (GATK 4.1.4.1, Python 3.7.7, R 4.0)
    • R / Bioconductor (R 4.0, Bioconductor 3.11.0, Python 3.7.7)
  • To incorporate these changes, we have updated notebook environments to a new default image and changed the labelling as follows:
    • "New Default (Released on January 14): (GATK 4.1.4.1, Python 3.7.7, R 3.6.3)" label has been changed to "Legacy GATK (default prior to May 14): (GATK 4.1.4.1, Python 3.7.7, R 3.6.3)".
    • "Bioconductor (Python 3.7.7, R 3.6.3, BioCVersion 3.10.1, tidyverse 1.3.0)" label has been changed to "Legacy R / Bioconductor (R 3.6.3, Bioconductor 3.10, Python 3.7.7)".
    • "Legacy: (default prior to January 14)" label has been changed to "Legacy Python/R (default used prior to January 14)".

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Comments

5 comments

  • Comment author
    Philipp Hahnel
    • Edited

    > Note that TSV functions in the Data tab does not currently work for sets of sets.

    It would be helpful to note this in the documentation. How is this currently supposed to be handled? I have a job that submits an array of tumor bams and an array of normal bams for each patient. I do not want to submit each job by hand. Uploading a tsv with three columns, each row of the form

    participant_id     [tumor1.bam, tumor2.bam]     [normal1.bam, normal2.bam]

    doesn't seem to parse the arrays correctly as each array is parsed as a string, not an array of strings.

    Thanks for any help on that!

    1
  • Comment author
    Derek Caetano-Anolles

    That's a good point, Philipp Hahnel; thanks for the question — I've discussed it with the team, and we will be making updates to the documentation soon.

    1
  • Comment author
    Philipp Hahnel

    Just as a follow-up note for importing arrays in TSVs: https://support.terra.bio/hc/en-us/community/posts/4405453406235/comments/4410978206363

    Documenting that they need to be JSON-valid is also helpful. Thanks!

    1
  • Comment author
    Allie Cliffe

    Philipp Hahnel Thanks for the feedback. I am sure you are not the only user who has struggled with this! I've added that warning to documentation on How to add an array to a data table. 

    0
  • Comment author
    Allie Cliffe

    Philipp Hahnel It is now possible to make sets of sets in the workspace data page:

    1. Open the set table
    2. Select the rows corresponding to the sets you want to make a set for
    3. Select "Edit" (the pencil icon) at the top left of the table
    4.  Select "Save selection as a set" from the menu

    Once you give your set a name, you will see a new set_set table!

     

    0

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