MultiQC

MultiQC configuration file

Type object
File match multiqc_config.yaml multiqc_config.yml .multiqc_config.yaml .multiqc_config.yml
Schema URL https://catalog.lintel.tools/schemas/schemastore/multiqc/latest.json
Source https://raw.githubusercontent.com/MultiQC/MultiQC/refs/heads/main/multiqc/utils/config_schema.json

Validate with Lintel

npx @lintel/lintel check
Type: object

Schema for MultiQC config validation

Properties

title string | null

Report title

Default: null
subtitle string | null

Report subtitle

Default: null
intro_text string | null

Report introduction text

Default: null
report_comment string | null

Report comment

Default: null
report_header_info object[] | null

Report header dictionary

Default: null
show_analysis_paths boolean | null

Show analysis paths in the report

Default: null
show_analysis_time boolean | null

Show analysis time in the report

Default: null
custom_logo_dark string | null

Path to custom logo image for dark mode

Default: null
custom_logo_url string | null

URL for custom logo

Default: null
custom_logo_title string | null

Title for custom logo

Default: null
custom_logo_width integer | null

Width in pixels for the custom logo

Default: null
custom_css_files string[] | null

Custom CSS files to include

Default: null
simple_output boolean | null

Simple output

Default: null
template string | null

Report template to use

Default: null
template_dark_mode boolean | null

Enable dark mode toggle and JavaScript for the report template

Default: null
plot_font_family string | null

Custom font family for plots (defaults to system font stack)

Default: null
profile_runtime boolean | null

Profile runtime

Default: null
profile_memory boolean | null

Profile memory

Default: null
pandoc_template string | null

Pandoc template

Default: null
read_count_multiplier number | null

Read count multiplier

Default: null
read_count_prefix string | null

Read count prefix

Default: null
read_count_desc string | null

Read count description

Default: null
long_read_count_multiplier number | null

Long read count multiplier

Default: null
long_read_count_prefix string | null

Long read count prefix

Default: null
long_read_count_desc string | null

Long read count description

Default: null
base_count_multiplier number | null

Base count multiplier

Default: null
base_count_prefix string | null

Base count prefix

Default: null
base_count_desc string | null

Base count description

Default: null
output_fn_name string | null

Output filename

Default: null
data_dir_name string | null

Data directory name

Default: null
plots_dir_name string | null

Plots directory name

Default: null
data_format string | null

Data format for output files

Default: null
force boolean | null

Overwrite existing reports

Default: null
verbose boolean | null

Verbose output

Default: null
no_ansi boolean | null

Disable ANSI output

Default: null
quiet boolean | null

Quiet output

Default: null
prepend_dirs boolean | null

Prepend directories to sample names

Default: null
prepend_dirs_depth integer | null

Depth to prepend directories

Default: null
prepend_dirs_sep string | null

Separator for prepended directories

Default: null
file_list boolean | null

Create a file list

Default: null
require_logs boolean | null

Require logs for reports

Default: null
version_check_url string | null

Version check URL

Default: null
make_data_dir boolean | null

Create data directory

Default: null
zip_data_dir boolean | null

Zip data directory

Default: null
data_dump_file boolean | null

Write data to a file

Default: null
data_dump_file_write_raw boolean | null

Write raw data to a file

Default: null
megaqc_url string | null

MegaQC URL to upload to

Default: null
megaqc_access_token string | null

MegaQC access token

Default: null
megaqc_timeout integer | null

MegaQC timeout

Default: null
export_plots boolean | null

Export plots

Default: null
export_plots_timeout integer | null

Timeout in seconds for exporting each plot to a static image (default: 60)

Default: null
make_report boolean | null

Make report

Default: null
make_pdf boolean | null

Make PDF

Default: null
ai_summary boolean | null

AI summary

Default: null
ai_summary_full boolean | null

AI summary full

Default: null
ai_provider string | null

AI provider

Default: null
ai_model string | null

AI model

Default: null
ai_custom_endpoint string | null

AI custom endpoint

Default: null
ai_auth_type string | null

AI auth type

Default: null
ai_retries integer | null

AI retries

Default: null
ai_extra_query_options string | null

AI extra query options

Default: null
ai_custom_context_window string | null

AI custom context window

Default: null
ai_prompt_short string | null

Prompt for short AI summary, put before the report details when sent to the provider

Default: null
ai_prompt_full string | null

Prompt for full AI summary, put before the report details when sent to the provider

Default: null
no_ai boolean | null

Disable AI

Default: null
ai_anonymize_samples boolean | null

Anonymize samples

Default: null
ai_reasoning_effort string | null

Reasoning effort level for OpenAI reasoning models (low, medium, high)

Default: null
ai_max_completion_tokens integer | null

Maximum completion tokens for OpenAI reasoning models

Default: null
ai_extended_thinking boolean | null

Enable extended thinking for Anthropic Claude 4 models

Default: null
ai_thinking_budget_tokens integer | null

Budget tokens for Anthropic extended thinking

Default: null
seqera_api_url string | null

Seqera API URL

Default: null
seqera_website string | null

Seqera website

Default: null
plots_force_flat boolean | null

Force static plot images

Default: null
plots_force_interactive boolean | null

Force interactive plots

Default: null
plots_export_font_scale number | null

Font scale for exported plots

Default: null
plots_flat_numseries integer | null

Number of series to show in flat plots

Default: null
plots_defer_loading_numseries integer | null

Number of series to defer loading - user will need to press button to render plot

Default: null
lineplot_number_of_points_to_hide_markers integer | null

Number of points to hide markers - sum of data points in all samples

Default: null
barplot_legend_on_bottom boolean | null

Place bar plot legend at the bottom (not recommended)

Default: null
boxplot_boxpoints string | boolean | null

Boxplot boxpoints setting

Default: null
box_min_threshold_outliers integer | null

For more than this number of samples, show only outliers

Default: null
box_min_threshold_no_points integer | null

For more than this number of samples, show no points

Default: null
violin_downsample_after integer | null

Downsample data for violin plot starting from this number os samples

Default: null
violin_min_threshold_outliers integer | null

For more than this number of samples, show only outliers

Default: null
violin_min_threshold_no_points integer | null

For more than this number of samples, show no points

Default: null
collapse_tables boolean | null

Collapse tables

Default: null
max_table_rows integer | null

Maximum number of rows to show in tables

Default: null
max_configurable_table_columns integer | null

Maximum number of columns to show in tables

Default: null
general_stats_columns Record<string, object>

Configuration for general stats columns per module. Keys are module IDs.

general_stats_helptext string | null

Help text for general statistics table.

Default: null
table_columns_visible object | null

Which columns to show in tables

Default: null
table_columns_placement object | null

Placement of columns in tables

Default: null
table_columns_name object | null

Name of columns in tables

Default: null
table_cond_formatting_colours object[] | null

Colours to use for conditional formatting in tables

Default: null
table_cond_formatting_rules object | null

Rules for conditional formatting in tables

Default: null
decimalPoint_format string | null

Decimal point format

Default: null
thousandsSep_format string | null

Thousands separator format

Default: null
remove_sections string[] | null

Sections to remove

Default: null
section_comments object | null

Comments for sections

Default: null
lint boolean | null

Lint

Default: null
strict boolean | null

Strict

Default: null
development boolean | null

Development

Default: null
custom_plot_config object | null

Custom plot config

Default: null
custom_table_header_config object | null

Custom table header config

Default: null
software_versions object | null

Software versions

Default: null
ignore_images boolean | null

Ignore images

Default: null
fn_ignore_dirs string[] | null

Directories to ignore

Default: null
fn_ignore_paths string[] | null

Paths to ignore

Default: null
sample_names_ignore string[] | null

Sample names to ignore

Default: null
sample_names_ignore_re string[] | null

Sample names to ignore (regex)

Default: null
sample_names_only_include string[] | null

Sample names to include

Default: null
sample_names_only_include_re string[] | null

Sample names to include (regex)

Default: null
sample_names_rename_buttons string[] | null

Sample names to rename

Default: null
sample_names_replace object | null

Sample names to replace

Default: null
sample_names_replace_regex boolean | null

Sample names to replace (regex)

Default: null
sample_names_replace_exact boolean | null

Sample names to replace (exact)

Default: null
sample_names_replace_complete boolean | null

Sample names to replace (complete)

Default: null
sample_names_rename string[][] | null

Sample names to rename

Default: null
show_hide_buttons string[] | null

Show/hide buttons

Default: null
show_hide_patterns string | string[][] | null

Show/hide patterns

Default: null
show_hide_regex string | boolean[] | null

Show/hide regex

Default: null
show_hide_mode string[] | null

Show/hide mode

Default: null
highlight_patterns string[] | null

Patterns for highlighting samples

Default: null
highlight_colors string[] | null

Colors to use for highlighting patterns

Default: null
highlight_regex boolean | null

Whether to use regex mode for highlighting

Default: null
no_version_check boolean | null

No version check

Default: null
log_filesize_limit integer | null

Log filesize limit

Default: null
filesearch_lines_limit integer | null

Filesearch lines limit

Default: null
report_readerrors boolean | null

Report read errors

Default: null
skip_generalstats boolean | null

Skip generalstats

Default: null
skip_versions_section boolean | null

Skip versions section

Default: null
disable_version_detection boolean | null

Disable version detection

Default: null
versions_table_group_header string | null

Versions table group header

Default: null
data_format_extensions object | null

Data format extensions

Default: null
export_plot_formats string[] | null

Export plot formats

Default: null
filesearch_file_shared string[] | null

Filesearch file shared

Default: null
custom_content object | null

Custom content

Default: null
fn_clean_sample_names boolean | null

Clean sample names

Default: null
use_filename_as_sample_name boolean | string[] | null

Use filename as sample name (can be bool for all modules or list for specific modules/patterns)

Default: false
fn_clean_exts string | CleanPattern[] | null

Extensions to clean from sample names

Default: null
fn_clean_trim string[] | null

Strings to trim from start/end of sample names

Default: null
extra_fn_clean_exts string | CleanPattern[] | null

Additional extensions to clean from sample names

Default: null
extra_fn_clean_trim string[] | null

Additional strings to trim from start/end of sample names

Default: null
sp object | null

Search patterns for finding tool outputs

Default: null
parquet_format string | null

Parquet table format. Long format has columns 'sample_name', 'metric_name' and 'val_raw', 'val_raw_type', 'val_str'. To select values for a certain metric, you need to filter based on its name. In contrast, the wide format has columns named after metrics, prefixed with table name and optional namespace. It's easier to for analytics, however, might hit limits on the maximal number of columns in certain edge cases, as well as have potential issues in case of mixed types (i.e. if some values are non-numeric, as Parquet requires a column to have a single type).

Default: null

Definitions

CleanPattern object

Pattern for cleaning sample names

pattern string required

Pattern to match

type string

Type of pattern matching to use

Default: "truncate"
Values: "truncate" "remove" "regex" "regex_keep"
module string | string[] | null

Module(s) to apply this pattern to

Default: null
GeneralStatsColumnConfig object

Configuration for a general stats column

title string | null

Column title

Default: null
description string | null

Column description

Default: null
namespace string | null

Column namespace

Default: null
scale string | null

Color scale

Default: null
format string | null

Number format

Default: null
min number | null

Minimum value

Default: null
max number | null

Maximum value

Default: null
ceiling number | null

Ceiling value

Default: null
floor number | null

Floor value

Default: null
shared_key string | null

Shared key name

Default: null
hidden boolean | null

Whether column is hidden by default

Default: null
placement number | null

Column placement order

Default: null
GeneralStatsModuleConfig object

Configuration for a module's general stats columns

columns Record<string, object>

Columns to show in general stats table. Keys are column IDs.

SearchPattern object

Search pattern configuration for finding tool outputs

fn string | null

Filename pattern to match

Default: null
fn_re string | null

Filename regex pattern to match

Default: null
contents string | string[] | null

File contents to match

Default: null
contents_re string | string[] | null

File contents regex pattern to match

Default: null
num_lines integer | null

Number of lines to search

Default: null
shared boolean

Allow file to be processed by multiple search patterns

Default: false
skip boolean

Skip this search pattern

Default: false
max_filesize integer | null

Maximum file size to process

Default: null
exclude_fn string | string[] | null

Exclude files matching this pattern

Default: null
exclude_fn_re string | string[] | null

Exclude files matching this regex pattern

Default: null
exclude_contents string | string[] | null

Exclude files containing this content

Default: null
exclude_contents_re string | string[] | null

Exclude files containing this regex content

Default: null