GenPipes 5.0.1 Release Notes

What’s new?

This is a major release of GenPipes! There are usage changes, some pipelines are merged into a single DNA sequencing pipeline, others have been deprecated. Refer to the details below:

  • GenPipes 5.x distribution is now based on Python packaging and can be installed using pip. Earlier versions were distributed in the form of Python modules.

  • GenPipes 5.x onward will only supports Python v3.11.1 and above.

  • The command syntax to run GenPipes deployed in the Digital Research Alliance of Canada, formerly Compute Canada (CCDB) servers, such as beluga, has changed. Pipelines are now invoked with genpipes <pipeline> -h instead of <pipeline>.py -h. See example below:

    • Old Format

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

    • New Format

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

  • When using GenPipes deployed on the Digital Research Alliance Canada servers such as beluga, a new 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.

    • Old Variable

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

    • New Variable

      $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.

  • 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.

  • Markdown style reports have been deprecated for all pipelines in v5.0.1 and have been replaced entirely with MultiQC reports.

  • The following are deprecated. Please use GenPipes v4.6.1 to run these pipelines/protocols.

  • TumorPair and DNASeq-High Coverage

    • These pipelines have been merged into the DNASeq pipeline, where they are available as protocols.

  • DNA Sequencing Pipeline

    • The DNA sequencing High Coverage and Tumor Pair pipelines are merged into DNA sequencing pipeline.

    • Enhanced to support seven protocols.

    • Use -t option to select one of the supported protocols: germline_snv, germline_sv, germline_high_cov, somatic_tumor_only, somatic_fastpass, somatic_ensemble, somatic_sv

  • Amplicon sequencing Pipeline

    • The dada2 protocol is now the default and is the only available protocol for this pipeline.

    • MultiQC reporting has been added.

  • RNA Sequencing Pipeline (De Novo)

    • The trinity protocol has been updated to support Trinity v2.15.1

    • rnammer has been replaced with infernal, in accordance with changes made in Trinotate v4.0.2

    • MultiQC reporting has been added.

  • Methylseq pipeline

    • A new protocol option is now available to use the gemBS aligner instead of Bismark for mapping and methylation calling process.

Quick! Where can I find it? I can’t wait!

Where is the detailed ChangeLog?

A ChangeLog (CHANGELOG.md) is available in the archive as well as in the repository.

Since we use git, there are many ways to get the details in many formats.

One of our preferred ways is to use a script written by the author of the Ray assembler: Sébastien Boisvert, which lists the commits by tag and author.

Enjoy our pipelines installed on the many Compute Canada clusters! We look forward to your feedback!