case-report - create PDF, HTML reports from CGW JSON output

Feature

• Takes the CGW JSON output file via standard input or specifying the file on the command line
• Can output both PDF and HTML version of the generated report
• When outputing the HTML version, all assets copied along with the html file
• Can create a copy of the default HTML and web assets to create customized versions of the report
• Let's you specify which templates and assets to use on the command line to override the defaults

Getting Started

You can install with both npm and yarn.

npm install -g @pierian/case-report

yarn global add @pierian/case-report

Usage

case-report is built to work with the CGW application prepared for use on appliance sequencers, like Illumina. The command can be part of a pipe-line, taking the standard CGW JSON output via standard input to generate the report.

$ cgw | case-report

Commands and Options

There are two commands available to use with case-report. You can always type case-report --help to see the available commands, and case-report [command] --help to see specific options available for each command.

Usage: case-report [command] [options]

Commands:
  copy [options]    copy the default templates/assets for customization
  create [options]  generate PDF case report output                 [aliases: c]

Options:
  --version  Show version number                                       [boolean]
  --help     Show help                                                 [boolean]

create - this is the default command, and will run by default if no command is given on the command line copy - this is used to create a local copy of the html templates and web related assets to create custom reports

create

The create command has the following command specific options.

case-report create [options]

generate PDF case report output

Options:
  --input, -i      path to CGW JSON data input file to process [defaults to
                   stdin]                                               [string]
  --output-path    path to folder to write output files
                                                      [string] [default: "/tmp"]
  --output-prefix  prefix to prepend to all generated output files
                                                          [string] [default: ""]
  --pdf            output PDF format report            [boolean] [default: true]
  --html           output HTML format report (folder, files and assets)
                                                      [boolean] [default: false]
  --template-path  path to custom HTML report template(s)               [string]

copy

The copy command will copy the HTML templates and default assets to the current working directory (ie, ./, the directory you run the command from). It has the following command specific options.

case-report copy [options]

copy the default templates/assets for customization

Options:
  --version    Show version number                                     [boolean]
  --help       Show help                                               [boolean]
  --templates  copy the template html files            [boolean] [default: true]
  --assets     copy the default assets (css, images, fonts)
                                                       [boolean] [default: true]

Configuring

case-report can be configure via command line options or through a .casereportrc file. The .casereportrc file is a JSON configuration file. The command will look for this file in the current working directory and then traverse up the directory path until it finds one.

If it doesn't find it while traversing it will then look to see if you've configured a path to the configuration file in the CASE_REPORT_CFG environment variable. Barring that not being defined, it will lastly look in your current user's home directory (~/).

All command line options are settable in the .casereportrc configuration file. Here's an example configuration file.

{
  "input": "./test/cgw-output.json",
  "template-path": "./data",
  "assets-path": "./data/assets",
  "output-path": "./output",
  "output-prefix": "pierian-"
}