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: https://bitbucket.org/mugqic/genpipes/src/master/README.md
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:
https://bitbucket.org/mugqic/genpipes/downloads/mugqic_pipelines-2.0.0.tar.gz
The module mugqic/mugqic_pipelines/2.0.0 is installed on abacus, guillimin and mammouth clusters.
The source code is in Bitbucket: