🤖 eggd_conductor configs 🤖

The files contained in the app_configs and assay_configs folders are essential for the running of eggd_conductor.

🔧 App configs 🔧

The files in this repository are placeholders for the actual app config files stored in DNAnexus as those contain tokens.

Other than that, those files contain:

• DEMULTIPLEX_APP_ID
• AUTH_TOKEN
• ASSAY_CONFIG_PATH
• SLACK_TOKEN
• SLACK_LOG_CHANNEL
• SLACK_ALERT_CHANNEL
• JIRA_EMAIL
• JIRA_TOKEN
• JIRA_QUEUE_URL
• JIRA_ISSUE_URL

🔧 Assay configs 🔧

The assay config file for the conductor app is designed to be written as a JSON file, with each workflow or apps defined as an executable. For each workflow/app, there are several required and optional keys to add, with a required structure. Each assay requires its own assay config file to define all required executables and inputs, which are stored in DNAnexus under the ASSAY_CONFIG_PATH as defined in the app config file.

Full details on the assay config design and structure may be found here.

For each assay config file, there is both an assay_code and version field in the top level of the config. The assay_code determines if to use the config file for the current samples by checking for presence of the code in sample names, and the version is parsed to keep the highest version of each config file for each assay (this should follow semantic versioning).

To update an assay config file, a new copy of the file should be created in the respective assays directory. When updating the config, both the verion number in the version field of the config and the filename should be incremented, and the changelog should have a brief description added for the new version as to the changes made:

i.e.

• current file:

  # assay_configs/CEN/eggd_conductor_dias_CEN_config_v1.0.0.json
  
  {
    "name": "Config for CEN assay",
    "assay": "CEN",
    "assay_code": "EGG5",
    "version": "1.0.0",
    "details": "Includes main Dias workflow, single, multi, QC and reports",
    "changelog": {
        "v1.0.0": "Initial working version"
    },
    "demultiplex": true,
    ...
  

• new file:

  # assay_configs/CEN/eggd_conductor_dias_CEN_config_v1.1.0.json
  
  {
    "name": "Config for CEN assay",
    "assay": "CEN",
    "assay_code": "EGG5",
    "version": "1.1.0",
    "details": "Includes main Dias workflow, single, multi, QC and reports",
    "changelog": {
        "v1.0.0": "Initial working version",
        "v1.1.0": "Details on changes for v1.1.0"
    },
    "demultiplex": true,
    ...