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).
runtimes STR String of key-value pairs using : as a separator, indicating the execution runtimes for each task or workflow defined in workflow-url. For example, Main=m4-cluster:Main>Fq2Bam=m4-8xcluster. To list tasks/workflows for a given workflow, use the execs command. To find available runtime options, use the request runtimes-options command. (Optional, defaults to None, which runs the entire workflow using m4-cluster.)
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).
token_lifetime Specify the duration, in hours, for the SeqsLab API token lifespan for this run (optional, default = 2).
labels Specify labels for the run; multiple labels can be given with whitespaces as separators (optional).

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).
fastq_signature STR
Define a fastq path matching pattern using ~{} wrapping syntax for Runsheet column names. For example, ~{Sample_Name}_S~{Sample_ID} matches NA12878_S1.fastq.gz with Sample_Name as NA12878 and Sample_ID as 1 (optional, defaulting to ~{Sample_ID}).
token_lifetime Specify the duration, in hours, for the SeqsLab API token lifespan for this run (optional, default = 2).
seq-run-id Specify a runsheet header field as a sequencer run identifier; the specified value will be used as a sequencer run specific label for future jobs management (optional).

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).

runtime-options (rt)

List registered cluster runtimes settings.

output {json,table} Specify the output format of the stdout file (optional, default = json).
page Specify the page number in the set of paginated records (optional, default = 1).
page-size Specify the number of records to return in each page (optional, default = 10).

operator-pipelines (op)

List registered operator pipelines.

output {json,table} Specify the output format of the stdout file (optional, default = json).
page Specify the page number in the set of paginated records (optional, default = 1).
page-size Specify the number of records to return in each page (optional, default = 10).