nf-weblog plugin

This plugin allows Nextflow to send detailed workflow execution metadata and runtime statistics to a HTTP endpoint. To enable this feature, use the -with-weblog as shown below:

nextflow run <pipeline name> -with-weblog [url]

Or enable it in the Nextflow configuration:

weblog {
  enabled = true
  url = '...'
}

Workflow events are sent as HTTP POST requests to the given URL. The message consists of the following JSON structure:

{
  "runName": "<run name>",
  "runId": "<uuid>",
  "event": "<started|process_submitted|process_started|process_completed|error|completed>",
  "utcTime": "<UTC timestamp>",
  "trace": {  },
  "metadata": {  }
}

The JSON object contains the following attributes:

runName: The workflow execution run name.
runId: The workflow execution unique ID.
event: The workflow execution event. One of started, process_submitted, process_started, process_completed, error, completed.
utcTime: The UTC timestamp in ISO 8601 format.
trace: The task runtime information as described in the Trace report documentation. The set of included fields is determined by the trace.fields setting in the Nextflow configuration file. See the Trace configuration docs to learn more.

Included only for the following events: process_submitted, process_started, process_completed, error
metadata: The workflow metadata including the config manifest. For a list of all fields, have a look at the bottom message examples.

Included only for the following events: started, completed

Configuration

The following configuration options are available:

weblog.enabled

If true it will send HTTP POST requests to a given url.

weblog.url

The url where to send HTTP POST requests (default: http://localhost).

weblog.basicToken

A Basic authentication token to append to each HTTP request. It should be the user ID and password joined by a single colon, for example USER:PASSWORD.

Examples

Example `started` event

When a workflow execution is started, a message like the following is posted to the specified end-point. Be aware that the properties in the parameter scope will look different for your workflow. Here is an example output from the nf-core/hlatyping pipeline with the weblog feature enabled:

{
  "runName": "friendly_pesquet",
  "runId": "170aa09c-105f-49d0-99b4-8eb6a146e4a7",
  "event": "started",
  "utcTime": "2018-10-07T11:42:08Z",
  "metadata": {
    "params": {
      "container": "nfcore/hlatyping:1.1.4",
      "help": false,
      "outdir": "results",
      "bam": true,
      "singleEnd": false,
      "single-end": false,
      "reads": "data/test*{1,2}.fq.gz",
      "seqtype": "dna",
      "solver": "glpk",
      "igenomes_base": "./iGenomes",
      "multiqc_config": "/Users/sven1103/.nextflow/assets/nf-core/hlatyping/conf/multiqc_config.yaml",
      "clusterOptions": false,
      "cluster-options": false,
      "enumerations": 1,
      "beta": 0.009,
      "prefix": "hla_run",
      "base_index": "/Users/sven1103/.nextflow/assets/nf-core/hlatyping/data/indices/yara/hla_reference_",
      "index": "/Users/sven1103/.nextflow/assets/nf-core/hlatyping/data/indices/yara/hla_reference_dna",
      "custom_config_version": "master",
      "custom_config_base": "https://raw.githubusercontent.com/nf-core/configs/master"
    },
    "workflow": {
      "start": "2019-03-25T12:09:52Z",
      "projectDir": "/Users/sven1103/.nextflow/assets/nf-core/hlatyping",
      "manifest": {
        "nextflowVersion": ">=18.10.1",
        "defaultBranch": "master",
        "version": "1.1.4",
        "homePage": "https://github.com/nf-core/hlatyping",
        "gitmodules": null,
        "description": "Precision HLA typing from next-generation sequencing data.",
        "name": "nf-core/hlatyping",
        "mainScript": "main.nf",
        "author": null
      },
      "complete": null,
      "profile": "docker,test",
      "homeDir": "/Users/sven1103",
      "workDir": "/Users/sven1103/git/nextflow/work",
      "container": "nfcore/hlatyping:1.1.4",
      "commitId": "4bcced898ee23600bd8c249ff085f8f88db90e7c",
      "errorMessage": null,
      "repository": "https://github.com/nf-core/hlatyping.git",
      "containerEngine": "docker",
      "scriptFile": "/Users/sven1103/.nextflow/assets/nf-core/hlatyping/main.nf",
      "userName": "sven1103",
      "launchDir": "/Users/sven1103/git/nextflow",
      "runName": "shrivelled_cantor",
      "configFiles": [
        "/Users/sven1103/.nextflow/assets/nf-core/hlatyping/nextflow.config"
      ],
      "sessionId": "7f344978-999c-480d-8439-741bc7520f6a",
      "errorReport": null,
      "scriptId": "2902f5aa7f297f2dccd6baebac7730a2",
      "revision": "master",
      "exitStatus": null,
      "commandLine": "./launch.sh run nf-core/hlatyping -profile docker,test -with-weblog 'http://localhost:4567'",
      "nextflow": {
        "version": "19.03.0-edge",
        "build": 5137,
        "timestamp": "2019-03-28T14:46:55Z"
      }
    },
    "stats": {
      "computeTimeFmt": "(a few seconds)",
      "cachedCount": 0,
      "cachedDuration": 0,
      "failedDuration": 0,
      "succeedDuration": 0,
      "failedCount": 0,
      "cachedPct": 0.0,
      "cachedCountFmt": "0",
      "succeedCountFmt": "0",
      "failedPct": 0.0,
      "failedCountFmt": "0",
      "ignoredCountFmt": "0",
      "ignoredCount": 0,
      "succeedPct": 0.0,
      "succeedCount": 0,
      "ignoredPct": 0.0
    },
    "resume": false,
    "success": false,
    "scriptName": "main.nf",
    "duration": null
  }
}

Example `completed` event

When a task is completed, a message like the following is posted to the specified end-point:

{
  "runName": "friendly_pesquet",
  "runId": "170aa09c-105f-49d0-99b4-8eb6a146e4a7",
  "event": "process_completed",
  "utcTime": "2018-10-07T11:45:30Z",
  "trace": {
    "task_id": 2,
    "status": "COMPLETED",
    "hash": "a1/0024fd",
    "name": "make_ot_config",
    "exit": 0,
    "submit": 1538912529498,
    "start": 1538912529629,
    "process": "make_ot_config",
    "tag": null,
    "module": [

    ],
    "container": "nfcore/hlatyping:1.1.1",
    "attempt": 1,
    "script": "\n    configbuilder --max-cpus 2 --solver glpk > config.ini\n    ",
    "scratch": null,
    "workdir": "/home/sven1103/git/hlatyping-workflow/work/a1/0024fd028375e2b601aaed44d112e3",
    "queue": null,
    "cpus": 1,
    "memory": 7516192768,
    "disk": null,
    "time": 7200000,
    "env": "PATH=/home/sven1103/git/hlatyping-workflow/bin:$PATH\n",
    "error_action": null,
    "complete": 1538912730599,
    "duration": 201101,
    "realtime": 69,
    "%cpu": 0.0,
    "%mem": 0.1,
    "vmem": 54259712,
    "rss": 10469376,
    "peak_vmem": 20185088,
    "peak_rss": 574972928,
    "rchar": 7597,
    "wchar": 162,
    "syscr": 16,
    "syscw": 4083712,
    "read_bytes": 4096,
    "write_bytes": 0,
    "native_id": 27185
  }
}

Testing and debugging

To build and test the plugin during development, configure a local Nextflow build with the following steps:

Clone the Nextflow repository in your computer into a sibling directory:
```
git clone --depth 1 https://github.com/nextflow-io/nextflow ../nextflow
```
Configure the plugin build to use the local Nextflow code:
```
echo "includeBuild('../nextflow')" >> settings.gradle
```
(Make sure to not add it more than once!)
Compile the plugin alongside the Nextflow code:
```
make compile
```
Run Nextflow with the plugin, using ./launch.sh as a drop-in replacement for the nextflow command, and adding the option -plugins nf-weblog to load the plugin:
```
./launch.sh run nextflow-io/hello -plugins nf-weblog
```

Test endpoint

The echo.py script can be used to deploy a local server that logs POST requests, which is useful for testing the plugin:

./echo.py

Testing without Nextflow build

The plugin can be tested without using a local Nextflow build using the following steps:

Build the plugin: make buildPlugins
Copy build/plugins/<your-plugin> to $HOME/.nextflow/plugins
Create a pipeline that uses your plugin and run it: nextflow run ./my-pipeline-script.nf

Package, upload, and publish

The project should be hosted in a GitHub repository whose name matches the name of the plugin, that is the name of the directory in the plugins folder (e.g. nf-weblog).

Follow these steps to package, upload and publish the plugin:

Create a file named gradle.properties in the project root containing the following attributes (this file should not be committed to Git):
- github_organization: the GitHub organisation where the plugin repository is hosted.
- github_username: The GitHub username granting access to the plugin repository.
- github_access_token: The GitHub access token required to upload and commit changes to the plugin repository.
- github_commit_email: The email address associated with your GitHub account.
Use the following command to package and create a release for your plugin on GitHub:
```
./gradlew :plugins:nf-weblog:upload
```
Create a pull request against nextflow-io/plugins to make the plugin accessible to Nextflow.

Name		Name	Last commit message	Last commit date
Latest commit History 14 Commits
.github/workflows		.github/workflows
buildSrc		buildSrc
gradle/wrapper		gradle/wrapper
plugins		plugins
.gitignore		.gitignore
COPYING		COPYING
LICENSE		LICENSE
Makefile		Makefile
README.md		README.md
echo.py		echo.py
gradlew		gradlew
gradlew.bat		gradlew.bat
launch.sh		launch.sh
settings.gradle		settings.gradle

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nf-weblog plugin

Configuration

Examples

Example `started` event

Example `completed` event

Testing and debugging

Test endpoint

Testing without Nextflow build

Package, upload, and publish

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nf-weblog plugin

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Example started event

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Testing without Nextflow build

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