This topic provides examples on how to use Workflow Description Language (WDL).
Query the job list
Run the following command to query the list of jobs created for the WDL workflow:
ags wdl list
Expected output:
+----------+--------------------------+--------------------------------------+------------+
| JOB NAME | CREATE TIME | JOB ID | JOB STATUS |
+----------+--------------------------+--------------------------------------+------------+
| wf | 2020-10-21T06:34:10.859Z | 87546541-f41d-4745-9d1e-4b9b0f27b033 | Running |
| wf | 2020-10-21T05:52:28.360Z | cc195aee-41c7-44b0-89e5-4e94ba47f56b | Succeeded |
| wf | 2020-10-21T05:52:08.340Z | 7209675e-4277-4d68-8848-725abca6b143 | Succeeded |
| wf | 2020-10-21T03:50:01.010Z | 05ed1979-39d4-41db-8535-446919088a2b | Succeeded |
| wf | 2020-10-21T03:45:40.783Z | b2394c34-9086-441f-af49-02735b5710ed | Succeeded |
+----------+--------------------------+--------------------------------------+------------+
Query the details about a job
Run the following command to query the detailed information about a job:
Note The information includes the job ID and the path where the error log is stored.
ags wdl query cc195aee-41c7-44b0-89e5-4e94ba47f56b
Expected output:
{
"workflowName": "wf",
"workflowProcessingEvents": [
{
"description": "Finished",
"timestamp": "2020-10-21T05:53:05.109Z",
"cromwellId": "cromid-89e8e7d",
"cromwellVersion": "54-36be57c-SNAP"
},
{
"timestamp": "2020-10-21T05:52:28.359Z",
"cromwellVersion": "54-36be57c-SNAP",
"cromwellId": "cromid-89e8e7d",
"description": "PickedUp"
}
],
"metadataSource": "Unarchived",
"actualWorkflowLanguageVersion": "draft-2",
"submittedFiles": {
"workflow": "task bwa_mem_tool {\n String outputdir\n String fastqFolder\n String cpunum\n String bamfilename\n command {\n cd ${fastqFolder}\n cp gene.bam.bai gene.bam.bai.test\n }\n runtime {\n docker: \"registry.cn-beijing.aliyuncs.com/shuangkun/genetool:v1.1\"\n memory: \"2GB\"\n cpu: 1\n }\n }\ntask agstask {\n String config\n command {\n mkdir /root/.ags\n cp ${config} /root/.ags/\n ags remote list > /ags-wdl-nas/remote.txt\n }\n runtime {\n docker: \"registry.cn-beijing.aliyuncs.com/shuangkun/genetool:v1.1\"\n memory: \"2GB\"\n cpu: 1\n }\n }\nworkflow wf {\n call agstask\n call bwa_mem_tool\n} \n",
"root": "",
"options": "{\n\n}",
"inputs": "{\"wf.agstask.config\":\"/ags-wdl-nas/bwatest/ags/config\",\"wf.bwa_mem_tool.bamfilename\":\"gene.bam\",\"wf.bwa_mem_tool.cpunum\":\"6\",\"wf.bwa_mem_tool.fastqFolder\":\"/ags-wdl-nas/sample/MGISEQ2000_PCR-free_NA12878_1_V100003043_L01_1.fq.gz\",\"wf.bwa_mem_tool.outputdir\":\"/ags-wdl-nas/bwatest/output\"}",
"workflowUrl": "",
"labels": "{}"
},
"calls": {
"wf.bwa_mem_tool": [
{
"executionStatus": "Done",
"stdout": "/ags-wdl-nas/wf/cc195aee-41c7-44b0-89e5-4e94ba47f56b/call-bwa_mem_tool/execution/stdout",
"backendStatus": "Complete",
"commandLine": "cd /ags-wdl-nas/sample/MGISEQ2000_PCR-free_NA12878_1_V100003043_L01_1.fq.gz\ncp gene.bam.bai gene.bam.bai.test",
"shardIndex": -1,
"outputs": {},
"runtimeAttributes": {
"preemptible": "false",
"failOnStderr": "false",
"continueOnReturnCode": "0",
"docker": "registry.cn-beijing.aliyuncs.com/shuangkun/genetool:v1.1",
"maxRetries": "0",
"cpu": "1",
"memory": "2 GB"
},
"callCaching": {
"allowResultReuse": false,
"effectiveCallCachingMode": "CallCachingOff"
},
"inputs": {
"fastqFolder": "/ags-wdl-nas/sample/MGISEQ2000_PCR-free_NA12878_1_V100003043_L01_1.fq.gz",
"outputdir": "/ags-wdl-nas/bwatest/output",
"cpunum": "6",
"bamfilename": "gene.bam"
},
"returnCode": 0,
"jobId": "task-6dbeff7e",
"backend": "TESK",
"end": "2020-10-21T05:53:04.317Z",
"dockerImageUsed": "registry.cn-beijing.aliyuncs.com/shuangkun/genetool:v1.1",
"stderr": "/ags-wdl-nas/wf/cc195aee-41c7-44b0-89e5-4e94ba47f56b/call-bwa_mem_tool/execution/stderr",
"callRoot": "/ags-wdl-nas/wf/cc195aee-41c7-44b0-89e5-4e94ba47f56b/call-bwa_mem_tool",
"attempt": 1,
"executionEvents": [
{
"startTime": "2020-10-21T05:53:03.351Z",
"description": "UpdatingJobStore",
"endTime": "2020-10-21T05:53:04.317Z"
},
{
"startTime": "2020-10-21T05:52:29.408Z",
"endTime": "2020-10-21T05:52:29.408Z",
"description": "Pending"
},
{
"startTime": "2020-10-21T05:52:29.970Z",
"endTime": "2020-10-21T05:53:03.351Z",
"description": "RunningJob"
},
{
"endTime": "2020-10-21T05:52:29.957Z",
"startTime": "2020-10-21T05:52:29.408Z",
"description": "RequestingExecutionToken"
},
{
"description": "WaitingForValueStore",
"startTime": "2020-10-21T05:52:29.957Z",
"endTime": "2020-10-21T05:52:29.957Z"
},
{
"startTime": "2020-10-21T05:52:29.957Z",
"endTime": "2020-10-21T05:52:29.970Z",
"description": "PreparingJob"
}
],
"start": "2020-10-21T05:52:29.408Z"
}
],
"wf.agstask": [
{
"executionStatus": "Done",
"stdout": "/ags-wdl-nas/wf/cc195aee-41c7-44b0-89e5-4e94ba47f56b/call-agstask/execution/stdout",
"backendStatus": "Complete",
"commandLine": "mkdir /root/.ags\ncp /ags-wdl-nas/bwatest/ags/config /root/.ags/\nags remote list > /ags-wdl-nas/remote.txt",
"shardIndex": -1,
"outputs": {},
"runtimeAttributes": {
"preemptible": "false",
"failOnStderr": "false",
"continueOnReturnCode": "0",
"docker": "registry.cn-beijing.aliyuncs.com/shuangkun/genetool:v1.1",
"maxRetries": "0",
"cpu": "1",
"memory": "2 GB"
},
"callCaching": {
"allowResultReuse": false,
"effectiveCallCachingMode": "CallCachingOff"
},
"inputs": {
"config": "/ags-wdl-nas/bwatest/ags/config"
},
"returnCode": 0,
"jobId": "task-1aa59269",
"backend": "TESK",
"end": "2020-10-21T05:53:03.297Z",
"dockerImageUsed": "registry.cn-beijing.aliyuncs.com/shuangkun/genetool:v1.1",
"stderr": "/ags-wdl-nas/wf/cc195aee-41c7-44b0-89e5-4e94ba47f56b/call-agstask/execution/stderr",
"callRoot": "/ags-wdl-nas/wf/cc195aee-41c7-44b0-89e5-4e94ba47f56b/call-agstask",
"attempt": 1,
"executionEvents": [
{
"startTime": "2020-10-21T05:52:29.965Z",
"description": "RunningJob",
"endTime": "2020-10-21T05:53:02.773Z"
},
{
"description": "PreparingJob",
"startTime": "2020-10-21T05:52:29.957Z",
"endTime": "2020-10-21T05:52:29.965Z"
},
{
"description": "WaitingForValueStore",
"startTime": "2020-10-21T05:52:29.957Z",
"endTime": "2020-10-21T05:52:29.957Z"
},
{
"startTime": "2020-10-21T05:52:29.408Z",
"endTime": "2020-10-21T05:52:29.957Z",
"description": "RequestingExecutionToken"
},
{
"startTime": "2020-10-21T05:52:29.408Z",
"description": "Pending",
"endTime": "2020-10-21T05:52:29.408Z"
},
{
"endTime": "2020-10-21T05:53:03.297Z",
"startTime": "2020-10-21T05:53:02.773Z",
"description": "UpdatingJobStore"
}
],
"start": "2020-10-21T05:52:29.408Z"
}
]
},
"outputs": {},
"workflowRoot": "/ags-wdl-nas/wf/cc195aee-41c7-44b0-89e5-4e94ba47f56b",
"actualWorkflowLanguage": "WDL",
"id": "cc195aee-41c7-44b0-89e5-4e94ba47f56b",
"inputs": {
"wf.agstask.config": "/ags-wdl-nas/bwatest/ags/config",
"wf.bwa_mem_tool.fastqFolder": "/ags-wdl-nas/sample/MGISEQ2000_PCR-free_NA12878_1_V100003043_L01_1.fq.gz",
"wf.bwa_mem_tool.outputdir": "/ags-wdl-nas/bwatest/output",
"wf.bwa_mem_tool.cpunum": "6",
"wf.bwa_mem_tool.bamfilename": "gene.bam"
},
"labels": {
"cromwell-workflow-id": "cromwell-cc195aee-41c7-44b0-89e5-4e94ba47f56b"
},
"submission": "2020-10-21T05:52:13.812Z",
"status": "Succeeded",
"end": "2020-10-21T05:53:05.109Z",
"start": "2020-10-21T05:52:28.360Z"
}
Mount a PV
- Log on to the ACK console.
- In the left-side navigation pane of the ACK console, click Clusters.
- On the Clusters page, find the cluster that you want to manage and click the name of the cluster or click Details in the Actions column. The details page of the cluster appears.
- In the left-side navigation pane of cluster details page, choose .
- On the Helm page, find the release name ack-ags-wdl and click Update in the Actions column.
- In the Update Release dialog box, mount a persistent volume (PV) to the cluster. The naspvc3 PV is used
as an example.