JAWS TEAMS

We’re introducing a new feature in JAWS called “JAWS Teams.” This feature allows for easier management of users and offers a centralized location for sharing and delivering output files for each team.

  • List all the teams available:

jaws teams list
[
    "gt-ga",
    "nmdc",
    "dsi-ii",
    "sc-mcr",
    "gt-seqtech",
    "dsi-aa",
    "gt-syn",
    "phytzm"
]

  • List the teams to which you belong:

jaws teams my-teams
[
    "dsi-aa"
]

  • List the users associated with a team:

jaws teams members dsi-aa
[
    "dcassol",
...
]

  • Get a team’s site config - Outputs path:

jaws teams get-site dsi-aa dori
"/clusterfs/jgi/scratch/dsi/aa/jaws/dori-staging/dsi-aa"

  • Team’s owner has power and responsibilities, such as setting the path for each site, adding and deleting users from the team:

jaws teams set-site <TEAM_ID> <SITE_ID> <PATH>
jaws teams add-user <TEAM_ID> <USER_ID>
jaws teams del-user <TEAM_ID> <USER_ID>

How to use Jaws Teams?

When submitting a new run, you can use --team flag. The outputs for this run will be transferred to the team’s path.

jaws submit align_final.wdl inputs.json dori --team=dsi-aa

As an easy alternative, you can set the default_team at your jaws.conf file:

vi ~/jaws.conf

[USER]
token = <TOKEN>
default_team = dsi-aa

Important: Do not use quotes for the team’s name.

The Jaws Team’s new feature will transfer the final workflow outputs from cromwell-execution to the path defined for your team.

How do I find the output data?

jaws status <RUN_ID> will provide the path to final path. Please check output_dir.

Then, you can find the expected file tree structure:

/<TEAM PATH>/<RUN_ID>/<Cromwell_ID>

JAWS will copy the following in case of a successful run:

  • Workflow outputs;

  • Supplementary files:

    • errors.json;

    • metadata.json;

    • output_manifest.json;

    • outputs.json;

    • task_summary.json.

In case of a FAILED run, JAWS will skip the transfer of the output files. However, it’s possible to ‘force’ the download, by using jaws download <RUN_ID>. In this case, JAWS will copy the following:

  • Workflow outputs;

  • Supplementary files;

  • Failed tasks’ cromwell-execution folder only.

As we transition to copying the output files, we are deprecating out the jaws get command. To ensure backward compatibility, this command will remain functional for a few more months, serving solely to copy the final workflow outputs. However, please note that we plan to discontinue this command entirely in upcoming cycles.