Pipelines Reference Guide

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

Usage Change Effective v5.x onward

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 implements standardized genomics workflows, including DNA-Seq, tumour analysis, RNA-Seq, de novo RNA-Seq, ChIP-Seq, SARS-CoV-2 genome sequencing, methylation sequencing, Hi-C, capture Hi-C, and metagenomics. All pipelines have been implemented following a robust design and development routine by following established best practices standard operating protocols. The pipelines accept a binary sequence alignment map (BAM) or a FASTQ file as input.

This guide contains usage manual and reference information for all available GenPipes genomic analysis pipelines. Visit GenPipes Real-life Applications and use cases to see how these pipelines can be deployed for complex next-generation genomic analysis in real life scenarios.