General report

Configuration

The contents of the general report is defined by the configuration. This is defined under the configuration key general_report and should be a path to a yaml file that lists the items that should be presented in the report. The yaml file should define an array of object that can have the following properties:

Property	Required	Description
name	yes	The name of the item. Will the header for this item in the report.
description	yes	A description of the results. Will follow immediately after the header.
type	yes	The result type. Read more below.
input	yes	A relative path to the file defining the results.
nav_header	yes	The header in the navigation bar that the item should be a member of.
sections	no	Only used for type multiqc. Sections in the MultiQC report that should be extracted. Currently only table is supported.

The input field can contain sample and type wildcards.

Item types

The following types of items are supported:

Type	Input file type	Description
file_table	CSV or TSV file	The contents of the file will be rendered as a table.
image	PNG image	The image will be shown in the report.
plain_text	Plain text file	Presents the contents of the file as-is.
table	JSON file	Presents a JSON representation of a table as a table in the report. See format description below.
file_link	Any file	Presents a hyperlink to the file.
multiqc	MultiQC JSON file	Extracts and presents results for this sample from a MultiQC report.

JSON tables

The JSON for the tables should be represented as an array of objects where each object represents a row. For example, this table

column1	column2
row1	value1
row2	value2
row3	value3

would be represented as

[
    {
        "column1": "row1",
        "column2": "value1",
    },
    {
        "column1": "row2",
        "column2": "value2",
    },
    {
        "column1": "row3",
        "column2": "value3",
    }
]

Example configuration

files:
  - name: file_table
    type: file_table
    description: Comma or tab separated file
    input: path/to/file_table.csv
    nav_header: File types
  - name: plain_text
    type: plain_text
    description: plain text file
    input: path/to/plain_text.txt
    nav_header: File types
  - name: file_table (txt Tab-separated)
    type: file_table
    description: A tab separated txt file
    input: path/to/table.txt
    nav_header: File types
  - name: table
    type: table
    input: path/to/table.json
    description: Json file with json representation of a table
    nav_header: File types
  - name: file_link
    type: file_link
    input: reports/cnv_html_report/{sample}_{type}.pathology.cnv_report.html
    description: File link to other results
    nav_header: File types
  - name: image
    type: image
    input: path/to/image.png
    description: Image file
    nav_header: File types
  - name: MultiQC
    type: multiqc
    input: qc/multiqc/multiqc_DNA_data/multiqc_data.json
    sections: ["table"]
    description: multiqc general stats for this sample
    nav_header: File types

Ouput files

• reports/general_html_report/{sample}_{type}.general_report.html