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).
|
rerun
|
Rerun an existing run by calling the seqslab-api/wes/runs API. |
rerun-id
Specify the run-id that is going to be rerun (required).
workspace
Specify the workspace based on the signed in account (required).
|
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).
|
