GenPipes v6.1.1 Documentation

Usage Changes (from v5.x)

Using v4.x?

You are recommended to:

  • Review the changes in v5.x and v6.x (See tabs)

  • Migrate to using the latest GenPipes v6.x

What has Changed?

Following changes are effective from GenPipes release v6.x onward:

  • Requires Python v3.12.0 or higher.

  • A new environment variable ‘GENPIPES_INIS’ is introduced for streamlining access to the config files in the genpipes commands. In the future, ‘MUGQIC_PIPELINES_HOME’ will be deprecated. This is applicable when using GenPipes deployed on the DRAC servers such as Rorqual.

    • Before

      $MUGQIC_PIPELINES_HOME/pipelines/<pipeline>/<pipeline>.base.ini

    • Now

      $GENPIPES_INIS/<pipeline>/<pipeline>.base.ini

    Note

    Please note that the old variable, ‘MUGQIC_PIPELINES_HOME’ will still be accessible and is still in use for instructions on how to deploy GenPipes locally, in the cloud, or in a container.

  • A new Long Read DNA Sequencing pipeline is now available in v6.0 that supports three protocols:

    • Nanopore

    • Nanopore Paired Somatic

    • Revio

Following changes are effective from GenPipes release v5.x onward:

  • Starting with v5.0, GenPipes uses Python packaging and no longer relies on Python modules.

  • If you were using Python v2.7, you must upgrade to Python v3.11.1.

  • To run any GenPipes pipelines, use the new command syntax:

    • Old Format

      user@rorqual% <pipeline name>.py [options] -g genpipes_cmd.sh
user@rorqual% bash genpipes_cmd.sh

    • New Format

      user@rorqual% genpipes <pipeline name> [options] -g genpipes_cmd.sh
user@rorqual% bash genpipes_cmd.sh

  • RNA Sequencing (De Novo) pipeline has been updated in v5.0 release.

  • EpiQC pipeline, HiC-Seq pipeline, and AmpliconSeq qiime protocol have been deprecated starting v5.0 onward.

  • The DNA-Seq high coverage pipeline and the TumorPair pipeline have been merged into a single workflow DNA-Seq.

  • The Methylseq pipeline has a new protocol option using the gemBS aligner in addition to Bismark.

  • Genome build GRCh38 (human) is now the default reference genome for all pipelines, but other versions or species can be selected via config files, as before.

    Danger

    When using the mouse genome, please note that the annotation files for GRCm38 do not work with the Homer analysis. Use mm10, instead of the GRCm38 program.

  • Markdown style reports have been deprecated for all pipelines starting v5.0 onward and replaced entirely with MultiQC reports.

GenPipes is a flexible, Python-based, open-source framework optimized for genomic analysis using High-Performance Computing (HPC) cluster and cloud environments. It supports the development and deployment of multi-step, scalable, validated genomic workflows. Various genomics applications utilize its gene sequencing pipelines.

Sponsors

GenPipes is developed and financed by the Canadian Centre for Computational Genomics (C3G).

C3G is a core platform affiliated with McGill University, provides bioinformatics analysis and HPC services for life sciences research.

These services include:

  • Bespoke pipeline development

  • Fee-based analyses

  • Other suite of software solutions genomics

This documentation serves both new and experienced genomics users.

We welcome community contributions to GenPipes and its documentation. To understand its structure, refer to the Site Map.

DRAC Server Access

To use GenPipes 6.1.0 on Digital Research Alliance of Canada (DRAC) servers, first log in and activate access to the necessary servers.

  • Rorqual

  • Narval

  • Fir

  • Nibi

  • Trillium

Fighting COVID-19

GenPipes offers two pipelines: CoVSeq for short-read sequencing (e.g., Illumina) and Nanopore_CoVSeq for long-read sequencing. These pipelines help researchers analyze viral sequences and detect mutations quickly, preventing the spread of new strains.

GenPipes Wizard

Introducing the GenPipes Wizard, our latest tool that helps beginners dive right into genomic analysis using GenPipes. This intuitive wizard walks new users through picking the best deployment option, pipeline, and protocol, while automatically assembling the complete command for running GenPipes

Overview

Documentation