GenPipes 2.0.0 Release Notes

May the genomic analysis and bioinformatics force be with you!

This is the first Python release of GenPipes!

What’s new?

  • Complete redesign of the pipelines in Python for DNA-Seq, RNA-Seq, RNA-Seq De Novo Assembly, PacBio Assembly. ChIP-Seq pipeline will be available in the next release.

  • Pipelines now share a common list of options

  • Option and step description is available with –help

  • Config .ini files can be provided as a list with default one set for abacus and Homo sapiens genome; custom ones can be added for other clusters and/or genomes; refer to latest configuration file details here.

  • 2 job schedulers are available to submit jobs: PBS for job submission on a cluster, batch for simple command line script

  • Smart job up-to-date status is computed given a step range: if a job is not up to date, all dependent subsequent jobs are created as well

  • Option to force job creation even if they are up to date

  • New input readset file format. Cf:

  • Log-leveled messages to track job creation, input/output files, up-to-date status

  • Bash script output with version, timestamp and number of created jobs

  • Option to specify output directory

  • and many more…

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

This version tarball is in:

The module mugqic/mugqic_pipelines/2.0.0 is installed on abacus, guillimin and mammouth clusters.

The source code is in Bitbucket: