本文介绍WDL工作流的帮助示例。

查询任务列表

输入以下命令,查询WDL工作流的任务列表。

ags wdl list

预期输出:

+----------+--------------------------+--------------------------------------+------------+
| 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  |
+----------+--------------------------+--------------------------------------+------------+

获取任务详细信息

输入以下命令,获取任务详细信息。
说明 您可以在任务详细信息中获取JOB ID、错误日志保存路径等信息。
ags wdl query cc195aee-41c7-44b0-89e5-4e94ba47f56b

预期输出:

{
    "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"
}

挂载PV

  1. 登录容器服务管理控制台
  2. 在控制台左侧导航栏中,单击集群
  3. 集群列表页面中,单击目标集群名称或者目标集群右侧操作列下的详情
  4. 在集群管理页左侧导航栏中单击发布
  5. 发布页面单击Helm页签,单击ack-ags-wdl操作列的更新
  6. 更新发布对话框的文本框中挂载PV,以下以naspvc3为例。
    1. 添加PV名称。
      更新发布对话框的文本框中找到naspvcs字段,在naspvcs字段下增加所要添加的PV名称。
      naspvcs:
      - naspvc1
      - naspvc2
      - naspvc3
    2. 添加PV配置内容。
      更新发布对话框的文本框添加PV配置内容,然后单击更新
      naspvc3:
        driver: csi
        mountOptions: nolock,tcp,noresvport
        mountVers: "3"
        nasbasepath: /ags-wdl-nas3
        path: /tarTest/sample
        server: xxxxxxxx.cn-beijing.nas.aliyuncs.com
      完成挂载PV后,后续创建的任务可以读取或写入新挂载的PV。