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 (optional).
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 (optional).
request-path STR
Specify the request.json file to run (optional).
|
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
|
Schedule a WES run with given date, time, and recurrence. |
request-path STR
Specify a previously scheduled run request ID (required).
date STR
Specify the schedule date, in the format of YYYY-MM-DD (required).
time STR
Specify the schedule time, in the format of HH-MM (required).
time-zone {UTC,LOCAL}
Specify the time zone for the provided date and time. If LOCAL is selected, the date and time will be
interpreted according to the operating system’s time zone. (optional, default = UTC).
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).
|
detail
|
Get WES run detail_config.json with a 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).
output-path STR
Specify the absolute output path for keeping the WES run detail_config.json. If not given, the command will return the detail_config.json to stdout (optional).
|
cancel
|
Cancel WES run based on run ID. |
run-id STR
Specify the run_id that is going to be cancelled (required).
workspace STR
Specify the workspace based on the signed in account (required).
|
delete
|
Delete WES run as well as all the generated output files based on run ID. |
run-id STR
Specify the run_id that is going to be delete (required).
workspace STR
Specify the workspace based on the signed in account (required).
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