maxulysse/compile-latex

Introduction

maxulysse/compile-latex is a lightweight Nextflow pipeline that compiles LaTeX documents into PDF using XeLaTeX.

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Provide the input tex file with the --input parameter.

Run the pipeline using:

nextflow run maxulysse/compile-latex \
   -profile <docker/singularity/.../institute> \
   --input file.tex \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Main parameters

• --input: Path to the input .tex file.
• --outdir: Output directory for results and reports.
• --outname: Optional output PDF filename.
• --biblio: Path to bibliography file (default: assets/biblio.bib).
• --pictures: Path to image folder (default: assets/pictures).

Output

After completion, the output directory contains:

• Compiled PDF file (<FILE>.pdf or --outname if provided)
• pipeline_info/ with execution reports (execution_report, execution_timeline, execution_trace, pipeline_dag) and run parameters (params.json)

Example: example.pdf

Credits

maxulysse/compile-latex was originally written by Maxime U Garcia for his own usage. And testing around things with Nextflow and nf-core.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

If you use maxulysse/compile-latex for your analysis, please cite it using the following doi: 10.5281/zenodo.1155669

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.