Altocumulus

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Command line utilities for running workflows on Terra or Cromwell including:

  • Run a Terra method, and bulk add/delete methods on Terra.

  • Submit WDL workflow jobs to a sever running Cromwell, as well as check jobs’ status, abort jobs, and get logs.

  • Replace local file paths with remote Cloud (Google Cloud or Amazon AWS) bucket URIs, and automatically upload referenced files to Cloud buckets.

  • Parse monitoring log files to determine optimal instance type and disk space.

Important tools used by Altocumulus:

Version 2.3.0 June 21, 2023

  • Add cromwell get_task_status command to get a summary JSON file on the status of all WDL tasks of a job.

Version 2.2.0 November 4, 2022

  • In cromwell run command, automatically create zip file on dependency WDLs for a local WDL workflow.

  • Remove query command.

  • Bug fix.

Version 2.1.2 August 15, 2022

  • Bug fix on BCL folder and FASTQ file uploading. [PR #30]

  • In cromwell list_jobs command, assign informative names for jobs with nan workflow name. [PR #31 and #32]

Version 2.1.1 August 12,2022

  • Add --type option to query command to specify query type.

Version 2.1.0 August 4, 2022

  • Altocumulus now only works with Python 3.8+.

  • Improve FASTQ file uploading. [PR #28]

  • Add query command to query project metadata from a LIMS (Laboratory Information Management System) via RESTful APIs.

Version 2.0.3 May 24, 2022

  • Support uploading only the FASTQ files with filename prefix specified within the source folder, instead of the whole folder, to the Cloud. [PR #24]

  • In cromwell list_jobs command, add -n option to show only top n jobs. [PR #21]

  • Bug fix:

    • Make all the temporary files with filenames unique per process, and remove them even when submission fails.

    • Fix the issue in cromwell list_jobs command when workflows’ names are not returned by Cromwell API. [PR #20 by Asma Bankapur]

    • Fix the issue in cromwell get_logs command when no subworkflow exists in a WDL subtask call. [PR #22]

Version 2.0.2 March 16, 2022

  • Fix the issue when submitting jobs using Dockstore workflow without specifying version (i.e. implicitly using default version):

    • Dockstore API points to an incorrect path in the top-level workflow_path value.

    • So always search through all versions to use the corresponding workflow_path inside the default version entry.

Version 2.0.1 March 1, 2022

  • Add --profile option to allow use a specific AWS profile when dealing with AWS backend:

    • In terra command: run and get_logs sub-commands.

    • In upload command.

  • In cromwell run sub-command:

    • Add -d option to allow attach dependency WDL files along with the main workflow WDL file specified in -m option.

    • Fix the issue on processing floating numbers in workflow input JSON files.

Version 2.0.0 January 12, 2022

  • Make method-related commands in legacy version as sub-commands under terra command, including:

    • run, add_method, remove_method, storage_estimate.

  • Create sub-commands under cromwell command for interaction between users and Cromwell server, including:

    • run, check_status, abort, get_metadata, get_logs, list_jobs.

  • Make uploading local data to Cloud buckets a separate command upload.

  • Add parse_monitoring_log command to extract computing resource usage info from monitoring logs generated by Cumulus WDL workflows.

Version 1.1.1 September 3, 2021

Legacy version:

  • Make sure that float values would look the same as in JSON input. For example, if 0.00005 is given, altocumulus should pass 0.00005 instead of 5e-05 to Terra.