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Pangenome Graph Pipeline

Minimal example of a BioHackrXiv publication that can be generated with the Preview Service.

Step 1: Clone this Template Repository

This repository is a template repository. This means that you can hit the green "Use this template" button (after logging in) to use it as a template to start a new BioHackrXiv Publication:

Screenshot of the green "Use this template" button.

Step 2: Configuring the Markdown

The publication Markdown is found in the paper/paper.md file. At the top you can edit the YAML code with metadata. It is important to get this part correct, because otherwise the PDF generation will fail. The metadata looks like this:

title: 'DBCLS BioHackathon 2024 Report for Project: Genome variation'
title_short: 'BioHackJP24: Genome variation'
tags:
  - Genomics
  - Human genetics
authors:
  - name: Toshiaki Katayama
    affiliation: 1
affiliations:
  - name: Database Center for Life Science, Research Organization for Information and Systems
    index: 1
date: 31 August 2024
cito-bibliography: paper.bib
event: BH24JP
biohackathon_name: "DBCLS BioHackathon 2024"
biohackathon_url:   "https://2024.biohackathon.org/"
biohackathon_location: "Fukushima, Japan, 2024"
group: Genome variation
# URL to project git repo --- should contain the actual paper.md:
git_url: https://github.com/biohackathon-japan/bh24-genome-variation
# This is the short authors description that is used at the
# bottom of the generated paper (typically the first two authors):
authors_short: Toshiaki Katayama \emph{et al.}

Which metadata to update?

To change

The following fields should be changed:

  • title
  • title_short
  • tags
  • authors
  • affiliations
  • date
  • group
  • authors_short

Particularly important to update is the following field, which should point to your clone of the template, instead of the template itself:

Step 3: Writing the article

A full Markdown example is given in paper/paper.md. This includes instructions how to include figures, tables, and annotate citations with the Citation Typing Ontology.

Step 4: Previewing the paper as PDF

This repository can be converted into a preview PDF with BioHackrXiv Preview Server. The preview website asks for the link to your repository and will automatically find the paper.md and create an PDF.