Release of GenPipes 6.0.0

[Mareike Janiak]

A new release of GenPipes, 6.0.0 is now available.

 

What's new? 

==========

This is a major release : 

* General

     - GenPipes has moved from Bitbucket to GitHub: https://github.com/c3g/GenPipes

     - the python packaging has been improved with the inclusion of a pyproject.toml

* ChIPSeq

     - Two new metrics generated by DeepTools (Fingerplot QC and Correlation Matrix) are part of the chipseq protocol and included in the MultiQC report

* LongRead DNASeq

     - a new pipeline for analyzing long-read sequences

     - includes two protocols, revio (PacBio Revio) and nanopore (ONT Nanopore)

     - the nanopore protocol of this new pipeline is equivalent to the Nanopore pipeline that was available as a standalone pipeline in previous versions

* Nanopore

      - this pipeline is now deprecated, as it has been absorbed into the LongRead DNASeq pipeline as a protocol

* RNASeq

     - fixed errors that occurred when running the rnaseq_cancer protocol with single end reads

* Prologues and Epilogues

     - the prologues and epilogues found in the GenPipes output files have been revamped and standardized, so they are now the same for SLURM and PBS clusters

* Log Reports

     - it is now easier to generate log reports for GenPipes runs, regardless of whether you're working on PBS or SLURM clusters

     - formerly, log reports were generated with one of two scripts, depending on the cluster, but now a single command can be used on all clusters to generate a report of the status of each job in the GenPipes pipeline:

genpipes tools log_report --tsv log.out job_output/{PIPELINE}_job_list_{DATE}T{TIME}

      - for more information on log reports please visit the documentation

* Validate input files

      - a new tool is available to check the format of your readset and design files

      - genpipes tools validate_genpipes looks for missing columns, formatting errors, and trailing whitespaces, issues that are common sources of errors

Where to find it?

============ 

* The source code for this version is in bitbucket : 

https://github.com/c3g/GenPipes/releases/download/6.0.0/c3g_genpipes-6.0.0.tar.gz

* GenPipes is distributed as a package via pypi:

https://pypi.org/project/c3g-genpipes/

* The module genpipes/6.0.0 is installed on Abacus (MGC), Béluga, Graham, Cedar and Narval Alliance clusters.

 

* The source code is on GitHub :

https://github.com/c3g/GenPipes 

 

* For more documentation, please refer to :

https://genpipes.readthedocs.io/

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. 

The CHANGELOG.md is an overview of notable changes generated by auto-changelog:

https://github.com/CookPete/auto-changelog

--

Mareike Janiak

Bioinformatics Analyst - Technical Development

Canadian Centre for Computational Genomics (C3G)