Configuration Reference¶

Complete reference for the 00_CONFIG.yml configuration file.

Generated Template¶

When you run rxiv init, the following configuration file is created:

# Manuscript Configuration
# See https://rxiv-maker.henriqueslab.org for full documentation

title: "Your Manuscript Title"

authors:
  - name: "Your Name"
    email: "[email protected]"
    orcid: "0000-0000-0000-0000"
    affiliation: "Your Institution"

keywords:
  - keyword1
  - keyword2
  - keyword3

# Citation style: "numbered" for [1] or "author-date" for (Author, Year)
citation_style: "numbered"

Essential Fields¶

These fields should be customized for every manuscript:

`title`¶

The full title of your manuscript. This appears on the first page and in PDF metadata.

title: "A Novel Approach to Single-Cell Proteomics Using Mass Spectrometry"

`authors`¶

A list of authors with their details. Each author can have:

Field	Required	Description
`name`	Yes	Full name
`affiliation`	Yes	Institution name or affiliation ID (see below)
`email`	No	Contact email
`orcid`	No	ORCID identifier
`corresponding`	No	Set to `true` for the corresponding author

authors:
  - name: "Alice Smith"
    affiliation: "1"
    email: "[email protected]"
    orcid: "0000-0001-2345-6789"
    corresponding: true
  - name: "Bob Jones"
    affiliation: "1,2"

When using affiliation IDs (like "1", "2"), define them separately:

affiliations:
  - id: "1"
    name: "Department of Biology, University of Example"
  - id: "2"
    name: "Institute for Advanced Studies"

Alternatively, write the affiliation name directly:

authors:
  - name: "Alice Smith"
    affiliation: "Department of Biology, University of Example"

`keywords`¶

A list of keywords for your manuscript:

keywords:
  - proteomics
  - single-cell analysis
  - mass spectrometry

`citation_style`¶

Controls how citations appear in the text:

Value	Appearance	Example
`"numbered"`	Numeric references	`[1]`, `[2,3]`
`"author-date"`	Author-year format	`(Smith, 2023)`

Optional Fields¶

These fields have sensible defaults and can be added as needed.

Document Metadata¶

short_title: "Single-Cell Proteomics"    # Appears in page headers
abstract: "Your abstract text here"       # Or auto-extracted from ## Abstract section
bibliography: "03_REFERENCES.bib"         # Default bibliography file

Note: the abstract is automatically extracted from the ## Abstract section in 01_MAIN.md if not specified here.

Formatting Options¶

line_numbers: false          # Add line numbers to margins
draft_watermark: false       # Add "DRAFT" watermark
two_column: false            # Two-column layout
font_size: 10                # Font size in points (10, 11, 12)
paper_size: "a4paper"        # "a4paper" or "letterpaper"

Figure Settings¶

figures:
  directory: "FIGURES"       # Directory containing figure scripts
  generate: true             # Whether to run figure generation scripts
  formats: ["png", "svg"]    # Output formats for generated figures

Caching¶

cache:
  enabled: true              # Cache generated figures for faster rebuilds
  ttl_hours: 24              # How long cached figures remain valid

Validation¶

validation:
  enabled: true              # Run manuscript validation before building
  strict: false              # Fail on warnings (not just errors)
  skip_doi_check: false      # Skip DOI resolution checking

Methods Placement¶

methods_placement: "after_bibliography"

Options: "inline" (within main text), "after_results", "after_bibliography"

Bibliography Author Format¶

bibliography_author_format: "lastname_initials"

Value	Output
`"lastname_initials"`	Smith, J.A.
`"lastname_firstname"`	Smith, John A.
`"firstname_lastname"`	John A. Smith

Submission Settings¶

arxiv_category: "q-bio.QM"          # arXiv category for submission
preprint_server: "biorxiv"           # Target preprint server
acknowledge_rxiv_maker: true         # Add rxiv-maker acknowledgment

Complete Example¶

A fully configured manuscript for a multi-author bioRxiv preprint:

title: "Deep Learning for Automated Cell Segmentation in Fluorescence Microscopy"
short_title: "DL Cell Segmentation"

authors:
  - name: "Alice Smith"
    affiliation: "1"
    email: "[email protected]"
    orcid: "0000-0001-2345-6789"
    corresponding: true
  - name: "Bob Jones"
    affiliation: "1,2"
    orcid: "0000-0002-3456-7890"
  - name: "Carol Williams"
    affiliation: "2"

affiliations:
  - id: "1"
    name: "Department of Bioengineering, University of Example, London, UK"
  - id: "2"
    name: "Francis Crick Institute, London, UK"

keywords:
  - deep learning
  - cell segmentation
  - fluorescence microscopy
  - image analysis

citation_style: "numbered"
line_numbers: true
preprint_server: "biorxiv"

figures:
  generate: true

cache:
  enabled: true

methods_placement: "after_bibliography"
bibliography_author_format: "lastname_initials"