Release Notes

JAWS Release 7/2024 - 11/12/2024

✨ New Features and Improvements

KBase Site: A new JAWS site, kbase, has been added. This site is located at the NERSC cluster and is dedicated to supporting the KBase project.
Team-Based Site Permissions: Teams are now required to obtain permissions to use certain sites. Below is a summary of permissions granted to each team across sites: (Issue 237)
- JAWS Teams with Access to Dori, Perlmutter, JGI, and Tahoma:
  - gt-ga, dsi-ii, bionano, sc-mcr, dsi-syseng, workshop, plant_ha, mycocosm, plantcompgen, gaa, gt-seqtech, funcgen, sc-mds, gt-usa, micro-scale, rqc, dsi-aa, gt-syn, phytzm
- KBase Team: Can submit to jgi and kbase sites
- NMDC Team: Can submit to nmdc and nmdc_tahoma sites
- ORNL Team: Can submit to the defiant site
WDL URLs and Subworkflows: Users can now submit WDLs as URLs, with support for subworkflows that can either be relative paths or full URLs. (Issue 224)
jaws submit https://code.jgi.doe.gov/advanced-analysis/test-repo/-/raw/main/main.wdl dori

Please make sure the repository is public and provide the raw URL to the WDL argument.

jaws purge Command: Added the jaws purge command, allowing users to delete cromwell-execution folders for their own runs or those of team members, improving storage management. (Issue 235)
jaws status command is now brief by default, with the –verbose flag available for additional details. The help message for the –verbose flag has also been updated for clarity. (Issue 239 and Issue 229)
A clearer error message is now provided when a user submits jaws submit <wdl> <inputs> but omits the SITE argument. (Issue Client-214)
jaws-history command now has a –verbose flag, which defaults to False for a streamlined output. (Issue 227)
If the WDL tasks runtime_minutes is not specified, Cromwell will default to 35 minutes. We highly recommend specifying the runtime_minutes in the WDL file. (Issue Cromwell-175).
jaws tasks command now displays input and output sum sizes for each task in bytes. (Issue 1841).

🐛 Bug Fixes

jaws tasks command: - jaws tasks command now works on Tahoma. - Fixed an issue where jaws tasks did not display all tasks for a run.
The copy progress bar is now functional again for the jaws submit command.
Links in the documentation have been updated for deprecated functions to ensure accurate guidance (Issue 245).
Resolved an issue with the jaws validate <WDL> <inputs> command (Issue 232).
The result field in jaws status now resets to NULL when a run is resubmitted, providing accurate tracking of resubmissions (Issue 209).
Fixed an error where JAWS would attempt to validate subworkflows located in nested directories, ensuring proper workflow validation (Issue 213).
Improved the error message for failed container pulls, providing clearer troubleshooting information. (Issue 183).
Fixed an issue where JAWS did not update the container image when a tag was reused with a new SHA, ensuring that updated containers are recognized (Issue 176).

JAWS Release 6/2024 - 09/17/2024

✨ New Features

Supplementary files are now downloaded to user JAWS Teams directory upon run failure (Issue 210).

🐛 Bug Fixes

Users can now delete their own folders, specifically the <JAWS RUN ID> folder, after completing a local transfer on Dori (input and compute site are the same). (Issue 1840).
jaws submit command will now throw an error if the user is not part of a JAWS team, preventing unauthorized access and enhancing security. (Issue 222).

JAWS Release 5/2024 - 09/10/2024

✨ New Features and Improvements

JAWS Client Python Library and Documentation:
- Added the JAWS Python library to the JAWS Client. This library provides a Python interface to interact with JAWS, allowing users to submit runs, check run status, and download outputs programmatically.
- The JAWS Client Python library documentation is available at JAWS API section. (Issue 205).
JAWS Staging Area Overview
- Input File Cache Validation:
  
  When a run is submitted, the JAWS Client copies the input files to a designated “JAWS staging area.” For subsequent submissions using the same input files, JAWS will reference the cached copies instead of re-copying them. If an input file content has changed but its filename remains the same, JAWS will detect this and provide an error message. Here is an example of the error message:
```
jaws submit --no-cache align_final.wdl inputs.json dori
Error initializing Run: Unable to copy input files:
/clusterfs/jgi/groups/dsi/homes/dcassol/jaws/jaws-tutorial-examples/data/sample.fasta is different from its cached version.
Submitting with this input file can affect previous runs.
Use --overwrite-inputs to force update the cached input files.
```
  This ensures that input consistency is maintained and prevents files linked to previous runs from being unintentionally modified. (Issue 220 and Issue 206).
- Overwrite Inputs:
  
  Users can explicitly provide the –overwrite-inputs flag if they wish to update cached input files with a new version. (Issue 220).
```
jaws submit --no-cache align_final.wdl inputs.json dori --overwrite-inputs
```

For more information about the JAWS Staging Area, please refer to JAWS documentation.

Display Return Code (RC) to the jaws tasks Command:

The jaws tasks command now includes the RC file content for each task. This improvement provides users with additional context when troubleshooting task failures. (Issue Jaws-Cromwell-168 and Issue 1832).
Updated 48-Hour Maximum Walltime on Perlmutter:

The maximum walltime for jobs on the Perlmutter compute system has been updated to 48 hours. (Issue 150).

Please check the waltime limit for all available JAWS sites here.

✨ Jaws Resiliency

Local Output File Transfer Optimization:

JAWS has transitioned from using parallel-sync to Python’s built-in shutil.copy for local output file transfers. This change addresses several performance and compatibility issues:
- parallel-sync was rewritten in version 2.0; this new version did not include a local transfer function.
- The last compatible version of parallel-sync was incompatible with Python 3.11 due to outdated dependencies like the brunch package.
- By switching to shutil.copy, JAWS now leverages optimized kernel-level fast copy calls, improving performance and reducing dependency on external libraries.
- In addition to shutil.copy, JAWS now uses filecmp.cmp to verify the integrity of local file transfers by comparing file attributes such as size, type, and modification time. This method is more CPU efficient than using md5sum and provides the same level of accuracy. (Issue 1819 and Issue 1818 and Issue 214).

🐛 Bug Fixes

Improved error messaging for JAWS cancel command to provide clearer guidance when the RUN_ID is missing. (Issue 199).
Display RC File Content with Timestamp:
- Added a print statement to stderr.submit that outputs the contents of the RC file along with a timestamp.
- This helps in debugging issues such as the Cromwell error (rc=79), where the RC file might initially show rc=0 but later be overwritten by Cromwell with a rc=79. (Issue 160).
Users can now delete their own folders, specifically the run-id folder, after completing a Globus download. (Issue 238).

⚖️ Policy Updates

Fair Share Policy Update:
- Updated the fair share policy for Dori, allowing a maximum of 30 runs per user on the Dori cluster. (Issue 1826).
Please notice that we update our time limits for all the sites. Please check the walltime limit for all available JAWS sites here. (Issue 1836).

Time Overhead

When Cromwell submits a task, HTCondor manages job scheduling by checking the queue for available resources. The JAWS Pool Manager monitors HTCondor and, when needed, requests new Slurm nodes. Once a compute node is available, HTCondor submits the task.

Due to a slight delay (a few seconds) in resource allocation, we build in a time buffer to ensure jobs get the full requested time. For example, instead of requesting the maximum 48 hours on Perlmutter, we request 47 hours and 45 minutes to account for the delay.

JAWS Release 4/2024 - 05/21/2024

✨ Jaws Resiliency

JAWS Central and its databases have been migrated to IGB.
We have deployed a new site, jaws defiant, at the Advanced Computing Ecosystem (ACE) testbed located at the Oak Ridge Leadership Computing Facility (OLCF).

JAWS Release 3/2024 - 05/08/2024

🐛 Bug Fixes

Fixed bug here multiple users sharing the same input file caused conflicts. (Issue 208)

JAWS Release 2/2024 - 05/01/2024

✨ New Features

NMDC Tahoma Site: We’ve added a new JAWS site: nmdc_tahoma. This new site is located at the EMSL cluster, and it is dedicated to supporting the NMDC project.

Enhanced Error Messaging: Improvements have been made to the error messages for backend task failures, providing clearer guidance for troubleshooting. (Issue Pool-Manager-118)

jaws history command has new filtering options, allowing searches by JSON file name (e.g., my_inputs.json), WDL file name, user, or tag, using flags such as –json-file, –wdl, –user, and –tag. (Issue 88)

🆕 New behavior for JAWS

Dori exvivo nodes will now be dedicated solely to large memory tasks, optimizing resource allocation and enhancing performance. (Issue 122)

If a Cromwell task returns a code of 79 (error code related to file system issues), JAWS will automatically retry the task once more. (Issue 139)

The JAWS_SITE environment variable is now exported within container environments for running tasks. This means you can use $JAWS_SITE from your WDL commands{} section for conditional statements (if $JAWS_SITE == "dori" then do something). (Issue 142)

Slack notification now contains the workflow_root field. (Issue 191)

🐛 Bug Fixes

Fixed bug where JAWS was not able to create a user subdirectory under the Teams dir. (Issue 1790)

Fixed bug for parallel copy files. Parallel copy happens in lieu of globus when submitting jobs to the same site as you submitted from. (Issue 1782)

Added retries for Jaws-site retrieving metadata from cromwell. (Issue 1787)

JAWS First Winter Release - 02/07/2024

✨ New Features

JAWS will issue a warning if a File type is hardcoded in the WDL file. (Issue 128)
We have implemented a validation process to ensure the WDL file aligns with the inputs.json file, using womtool. This validation occurs automatically upon submission and can also be triggered manually by executing the jaws validate command. (Issue 175)
jaws validate <WDL_FILE> <INPUTS_JSON>

🆕 New behavior for JAWS

We update the Fair-Share policies: (Issue 136)

Task-Level Control:

Limit: There’s now a maximum limit of 200 concurrent tasks per user.

Queue: Tasks submitted above the 200-task limit will enter a queue.

Only successful runs will be copied to the team’s directory. (Issue 154)

Our backend system (HTCondor) will attempt to execute a task twice under certain conditions. If your task exceeds its allocated time, or if JAWS-site needs to be reassigned to a new node (Perlmutter site), or due to some instability in the backend, we will automatically initiate a second attempt to run the task.

Important to note:

When the backend or Cromwell retries a task, the cromwell-execution folder will not be reset. In specific cases, this requires adding a verification process in your WDL command stanza. For example, if the command includes creating directories or specific files. Depending on the outcome, you’ll need to determine whether to force the directory or file to be recreated or to skip this step. (Issue Pool-Manager-110)

🐛 Bug Fixes

Fixed issue related to retrieving metadata from runs that contain over 1 million rows. (Issue Cromwell-137)

A user-friendly error message is displayed when an invalid run_id is entered in the jaws status <RUN_ID> or jaws log <RUN_ID> commands. (Issue 177)

Fixed file permission issue for files transferred to the team’s directory via Globus from a compute site that is different from the input site. (Issue 168 and 1739)

Fixed issue related to transferring very large output datasets. (Issue 1746)

Return an error message to the user when Cromwell submission fails. (Issue 1568)

Updated the refdata path for the NMDC site (/global/cfs/cdirs/m3408/refdata). (Issue 1756)

workflow_root: null bug is fixed. (Issue 1747)

Added a tag to the summary.json supplementary file. (Issue 1758)

Increased the length of the JSON basename field. (Issue 1776)

Fixed job_id column in the jaws task output. (Issue 1749)

JAWS Second Fall Release - 11/09/2023

✨ New Features

JAWS has incorporated support for specifying execution time in the runtime section. In addition to memory and cpu, you can now include the time required to run each task. The mandatory key for specifying this information is runtime_minutes.

runtime_minutes:

Accepted types: Int

Int: minutes. Example:
runtime {
  docker: "ubuntu@sha256:c9cf959fd83770dfdefd8fb42cfef0761432af36a764c077aed54bbc5bb25368"
  runtime_minutes: 60
  memory: "5G"
  cpu: 4
}
The benefit of specifying runtime_minutes is that it provides a guarantee that the task will be put on a node with sufficient time.

⚠️ If the WDL runtime section uses time as a key or doesn’t specify any time value, the workflow will still be accepted but without the assurance it will be allocated to a suitable node.
✨ JAWS Client Container is Available ✨
How to use:
Dori:
JAWS_USER_CONFIG=~/jaws.conf JAWS_CLIENT_CONFIG=/clusterfs/jgi/groups/dsi/homes/svc-jaws/dori-prod/jaws-prod.conf apptainer run docker://doejgi/jaws-client:latest jaws --help
Append to the end of your ~/.bashrc on DORI:
jaws() {
  JAWS_USER_CONFIG=~/jaws.conf JAWS_CLIENT_CONFIG=/clusterfs/jgi/groups/dsi/homes/svc-jaws/dori-prod/jaws-prod.conf apptainer run docker://doejgi/jaws-client:latest jaws "$@"
}
Perlmutter:
JAWS_USER_CONFIG=~/jaws.conf JAWS_CLIENT_CONFIG=/global/cfs/projectdirs/jaws/perlmutter-prod/jaws-prod.conf shifter --image=doejgi/jaws-client:latest jaws --help
Append to the end of your ~/.bashrc on NERSC:
jaws() {
  JAWS_USER_CONFIG=~/jaws.conf JAWS_CLIENT_CONFIG=/global/cfs/projectdirs/jaws/perlmutter-prod/jaws-prod.conf shifter --image=doejgi/jaws-client:latest jaws "$@"
}

🆕 New behavior for JAWS

In our ongoing efforts to enhance performance and maintain a robust, up-to-date environment, we will be discontinuing support for WDL Draft-2 version 12/1/2023.

We will display a ⚠️ warning message to notify you if you are still using the old version when submitting a run.

We strongly urge all users to update their WDL workflows to the Version 1.0 specification. If you have any questions, please schedule a pair programming session with our Team.

🐛 Bug Fixes

We added a new flag to jaws validate to show shellCheck linter validation. In addition, the output also now prints newlines for better readability.

Addressed the issue “noise” being printed to stderr for Dori runs. (Issue 130)

Increased allowed length of WDL and JSON filenames. (Issue 1744)

jaws health command is now operational again.

workflow_root: null bug is fixed. (Issue Jaws-Support-148)

JAWS First Fall Release - 10/09/2023

✨ New Features

Dori Exvivo nodes are now available for JAWS. JAWS is using the long queue (14 days) and can access up to 1.5 TB of memory. (Issue 83)

Globus endpoint is available for Perlmutter! 🎉 (Issue 1683)

This means that you are now able to submit from Perlmutter to Dori/Tahoma/JGI sites and vice-versa.
Teams output directory will include JAWS user ID and will have the following structure (Issue 137):
/<TEAM PATH>/<JAWS_USER_ID>/<RUN_ID>/<Cromwell_ID>
New command: jaws tasks <RUN_ID>:
jaws tasks 18279
#TASK_DIR       STATUS     QUEUE_START          RUN_START            RUN_END              QUEUE_MIN  RUN_MIN  CACHED  TASK_NAME          REQ_CPU  REQ_GB  REQ_MIN  CPU_HRS
call-alignment  succeeded  2023-10-02 16:55:07  2023-10-02 16:56:16  2023-10-02 16:56:22  1          0        False   bbtools.alignment  1        1                0.0
call-samtools   succeeded  2023-10-02 16:56:36  2023-10-02 16:56:55  2023-10-02 16:56:57  0          0        False   bbtools.samtools   1        1                0.0
jaws tasks integrate two previously distinct commands, jaws task-log and jaws task-summary. Be sure to explore the newly unified and enhanced features:

“cpu_hours” metric is now included in the jaws tasks command for each task and jaws status as an aggregation for the entire workflow upon run completion.

Cached tasks will now be recorded in the jaws tasks post run completion.

jaws tasks status is now updated appropriately when a run is cancelled.

jaws tasks now uses timestamps derived from the task log instead of using Cromwell metadata.
New command: jaws download <RUN_ID>:

If a run fails, JAWS will skip the transfer to team’s directory. However, if you need the cromwell-execution for debugging reasons, you can use our new command to ‘force’ the download of the run:
jaws download 18386
{
    "download_id": 8272,
    "id": 18386,
    "status": "download queued"
}


- Please notice that the run output will be transferred to the team's directory.
New command jaws get-user (Issue 107)

This command gets current user’s settings.
jaws get-user
{
    "email": "dcassol@lbl.gov",
    "name": "Daniela Cassol",
    "slack_id": "<Member_ID>",
    "teams": [
        "dsi-aa",
        "nmdc"
    ],
  "uid": "dcassol"
}
Bash commands employing curl is now working on Tahoma. (Issue 121)

Output directory will include a copy of the original WDL, input.json, and subworkflows-ZIP files, for reproducibility. (Issue 1710)

jaws status is now verbose by default. If you prefer the short version, please use jaws status --brief. To ensure backward compatibility, when you use the command jaws status --verbose, it will issue a warning and additionally display the output of jaws status.

JAWS is now using the latest version of Cromwell-85.

🐛 Bug Fixes

JAWS will not transfer workflow outputs to teams output location runs that were canceled by the user. (Issue 156)

Fixed teams output directory permissions when the submission and compute site are the same. (Issue 1712)

Fixed issue when workflow name and site are the same. (Issue 23)

jaws resubmit command is restricted to the members of the team who own the run. (Issue 148)

We have improved the error messaging for jaws resubmit, especially when the original submission failed. (Issue 116)

jaws status is now displaying local time zone. (Issue 151)

jaws status will report when a run was canceled by the user in the result field. (Issue 1714)

We are ignoring extra attributes to the runtime{} stanza, for example "runtime_minutes": "20". (Issue 118)

When a run is canceled, it will be recorded to jaws tasks <RUN_ID>. (Issue 120)

Fixed issues reporting the wrong task status in jaws tasks <RUN_ID> command.

Fixed error for transfers when file was named pipe instead of regular file. (Issue 1725)

When a run is resubmitted (jaws resubmit <RUN_ID>), JAWS will ensure that all the input files required are still available. (e.g., haven’t been purged). (Issue Jaws-Support-110)

When a run is resubmitted (jaws resubmit <RUN_ID>), JAWS will update access timestamp (atime) for input files, in order to avoid purging files prematurely. (Issue 1689)

Fixed bug when Cromwell submission fails during input processing and was not recognized by JAWS. (Issue 1711)

outputs.json supplementary file contain relpaths instead of abspaths. (Issue 1652)

🆕 New behavior for JAWS

In our ongoing efforts to enhance performance and maintain a robust, up-to-date environment, we will be discontinuing support for WDL Draft-2 version 11/1/2023.

We will display a ⚠️ warning message to notify you if you are still using the old version when submitting a run.

We strongly urge all users to update their WDL workflows to the Version 1.0 specification. If you have any questions, please schedule a pair programming session with our Team.

JAWS Cromwell configuration was updated, and now Container tags can be used for call caching (Issue Jaws-Cromwell-122, Issue Jaws-Client-156).

We recommended referencing containers by their SHA256 instead of tag (e.g., doejgi/bbtools@sha256:64088.. instead of doejgi/bbtools:latest). While using mutable or “floating” tags in tasks can be convenient in certain scenarios, it adversely impacts the reproducibility of a workflow. For instance, executing the same workflow with doejgi/bbtools:latest now, and then rerunning it in a month or a year, could result in the use of different container images.

If the command stanza uses $TMPDIR, it will have access to /tmp. Previous we set to execution/ directory (e.g., NFS). (Issue 110)

❌ Deprecated Commands

jaws task-log and jaws task-summary have been deprecated (Issue 161, Issue 1719).

These two commands have been merged and into a new command, jaws tasks.

For backward compatibility, jaws task-log will be reporting the output of jaws tasks.

⚠️ Known issues

If the submission and compute sites are different (for example, from Dori to Tahoma), there could still be permission issues in the team’s output directory. In this case, the transfer to the team’s directory happens via Globus, we need are looking into solutions for this problem.

JAWS Summer Release - 09/05/2023

We are releasing a new version of JAWS that includes breaking changes.

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 -–verbose <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.

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

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.

We have implemented parallel copying capabilities when both the submission and compute site are the same, for example, from Dori to Dori. This effectively resolves the delay issues associated with the ‘download queue.’

Slack Notifications

We replaced Email with Slack notifications when the run is completed.

How to set up Slack Notification?

Please set up your slack_webhook and update your JAWS account. Instructions on how to get your Slack webhook are available here.

jaws update-user –email=dcassol@lbl.gov --slack_id <Member_ID> --slack_webhook <WebHook_URL>

Call-caching Strategy

The call-caching strategy that we used was “xxh64”, and that required a lot of I/O operation to calculate the hash of the entire file content. Now, we replace that with “fingerprint”. fingerprint will take the last modified time, size, and hash from the first 10 mb with xxh64 to create a file fingerprint. Please be aware of that, and please let us know if you think that can cause any file collision when the task will use call-caching. If you want to read more about the call-caching and all the strategies please check here.

Additional minor features

Added --forcequeue flag option to jaws submit command. Users can force run submission when the site has been disabled;
Resubmitting a run will change the “result” filed to “resubmitted” for jaws status <run id> command;
We now parse the runtime{} parameter values correctly when there is a space (i.e., memory: “5 G”) ticket: #111;
/refdata is mounted correctly and accessible to the WDLs.

Special note about the DORI TEAMS Folders: For this release, Teams’ folders on Dori must be located at /clusterfs/jgi/scratch/dsi/aa/jaws/teams/. However, once the Globus endpoint changes have been completed, teams’ folders may be edited under the team’s scratch.

JAWS Summer Release Slides

Link to JAWS Calendar

JAWS Sprint Release - 04/12/2023

We released a new version of JAWS.

Here are the changes that are now on PROD:

Dori Jaws site is available for testing;

Create a config file in your HOME directory:
touch ~/jaws.conf
chmod 600 ~/jaws.conf

Copy your token from CORI:

[USER]
token = <copy your token from CORI and paste it here>

Module load jaws

module use /clusterfs/jgi/groups/dsi/homes/svc-jaws/modulefiles
module load jaws/dori-prod
jaws submit <WDL_FILE> <INPUTS> dor

NOTE:

Dori and Perlmutter have temporary Globus limitations (IT has not configured JAWS application Globus endpoints yet).
Temporary workaround:
- Because data transfer isn’t available, you must log in to the cluster (Dori or Perlmutter) and submit the run from there.
- You can use Globus endpoint to transfer your data from Cori to Dori, for example.

Deprecated commands

jaws outfiles
jaws outputs
jaws metadata
jaws errors

This is part of the effort to refactor jaws metadata command (uses cromwell metadata). As users are submitting large workflows (> 10k tasks), cromwell metadata became too expensive to query and would sometimes timeout. Instead, we now wait for the run to finish and then write some associated reports (e.g. errors, outfiles, and outputs) to disc. These json files are written to the run’s execution directory and returned to users via jaws get.

To find the report files:

jaws get <RUN_ID> <DEST>
ls <DEST>
<workflow>.wdl
<inputs>.json
errors.json
metadata.json
outfiles.json
outputs.json
task_summary.json

jaws task-log changed:
- task-log is now much faster and robust than before and will support runs with greater than 10k tasks.
- Even more than before, it is a real-time reflection of a run’s current status since it gets its information directly from the backend instead of using an intermediate metadata cromwell, which was a bottleneck.
- However, because it no longer uses cromwell’s metadata, there are no longer records for cached tasks since they did not actually execute. Therefore, the “cached” column was deleted.
- Limitation for Tahoma site: jaws task-log isn’t working properly for Tahoma due to the firewall between the compute and workflow node. We have a ticket open for this issue. However, this will not affect your run!
jaws task-summary
It only will be available after the run is finished.
jaws status –verbose
Two more fields: workflow_name and workflow_root
jaws validate
miniwdl is used instead of womtool for WDL validation.
jaws resubmit
New command available! Resubmit a run (at the same compute site).

Fixed bugs reported by users

runtime parameters can be on separate lines;
Fixed jaws get --flatten;
symlinks can be used for the path to the WDL (jaws submit <symlink>/my.wdl my.json dori)
When restarting cromwell service (i.e. upon release) will not interrupt active Runs;
Added job purging policies to the HTCondor backend so that it can automatically cancel tasks that stay in HOLD status for too long time.
Added --time-min SLURM option for requesting SLURM compute nodes with a shorter wall-clock-time on Perlmutter when maintenance is scheduled.

Release Notes

JAWS Release 7/2024 - 11/12/2024

✨ New Features and Improvements

🐛 Bug Fixes

JAWS Release 6/2024 - 09/17/2024

✨ New Features

🐛 Bug Fixes

JAWS Release 5/2024 - 09/10/2024

✨ New Features and Improvements

✨ Jaws Resiliency

🐛 Bug Fixes

⚖️ Policy Updates

JAWS Release 4/2024 - 05/21/2024

✨ Jaws Resiliency

JAWS Release 3/2024 - 05/08/2024

🐛 Bug Fixes

JAWS Release 2/2024 - 05/01/2024

✨ New Features

🆕 New behavior for JAWS

🐛 Bug Fixes

JAWS First Winter Release - 02/07/2024

✨ New Features

🆕 New behavior for JAWS

🐛 Bug Fixes

JAWS Second Fall Release - 11/09/2023

✨ New Features

🆕 New behavior for JAWS

🐛 Bug Fixes

JAWS First Fall Release - 10/09/2023

✨ New Features

🐛 Bug Fixes

🆕 New behavior for JAWS

❌ Deprecated Commands

⚠️ Known issues

JAWS Summer Release - 09/05/2023

JAWS Teams

How to use Jaws Teams?

How do I find the output data?

Jaws Fair-share policies

Slack Notifications

Call-caching Strategy

Additional minor features

JAWS Sprint Release - 04/12/2023

Here are the changes that are now on PROD:

Deprecated commands

Fixed bugs reported by users