Work Execution Service (WES) subcommands

Table 5 Jobs subcommands

Subcommand

Description

Argument

dryrun

Workflow dry run to see if the given request.json files are properly configured by calling seqslab-api/wes/runs/dryrun and seqslab-api/wes/runs/files API.

--working-dir (--dir)
Specify the working directory path that contains request.json (required).
--workspace STR
Specify the workspace based on the signed in account (required).

get

Get WES run information based on run ID.

--run-id STR
Specify a previously executed WES run ID (required).
--workspace STR
Specify the workspace based on the signed in account (required).

request

Create WES run request.

--run-name STR (--name)
Define the run name for a single run (required).
--working-dir (--dir)
Specify the absolute output directory for generated jobs request.json (required).
--workflow-url (--url)
Specify a TRS URL used for a single run (required).
--execs STR
Specify the execs.json needed to create a WES request. If not given, the command will get the execs.json from the TRS object specified by the workflow_url (optional, default = None).
--integrity
Specify whether to enable data and runtime integrity check for the workflow engine (optional, default = False).
--trust
Specify whether to enable content trust for container runtime (optional, default = False).

request-runsheet (runsheet)

Parse run_sheet.csv and create a job execution request.json file for each job run.

--working-dir STR, -o STR
Specify the absolute output directory for generated jobs request.json (required).
--run-sheet STR (-r)
Specify the absolute output path for Run Sheet (required).
--execs STR
Specify the execs.json needed for create WES request. If not given, the command will get the execs.json from the TRS object specified by the workflow_url (optional, default = None).
--integrity
Specify whether to enable data and runtime integrity check for the workflow engine (optional, default = False).
--trust
Specify whether to enable content trust for container runtime (optional, default = False).

run

Run a workflow by calling the seqslab-api/wes/runs API.

--working-dir (--dir)
Specify the working directory path that contains request.json (required).
--workspace STR
Specify the workspace based on the signed in account (required).
--response-path STR
Specify the path of response.json in relation to the working directory (required).

run-state (state)

Get WES run information based on run ID.

--run-id STR
Specify a previously executed WES run ID.
--workspace STR
Specify the workspace based on the signed in account (required).

schedule

Run a job based on a previously registered run request. Typically, the run request is designed for a scheduled job, where the FQN-DRS connection of sequencing samples are left blank for future runtime sample-resolving. Thus, by specifying sample-resolving rule, the run request can be used to serve scheduled job use case.

--run-request-id STR
Specify a previously scheduled run request ID (required).
schedule-tag
Specify a tag marked on previously uploaded samples for a scheduled job (required).
--workspace STR
Specify the workspace based on the signed in account (required).