Release 6.1.1

What's Changed

This is a minor release:

• General

  • when using the project tracking option, md5 checksums are now created in the json for all output files

• LongRead DNASeq

  • the platform parameter used for clairS can now be set via the config file
  • fixed non-unique nanoplot metrics output file names

• RNASeq

  • the table containing differential expression results now includes column names that indicate the source of the metric (edgeR or DESeq2)

• DNASeq

  • resolved an error that occurred in the verifybamID step when using WES data by adding the proper exome bed file
  • fixed path to custom djerba formatting files
  • resolved unwanted restarts of PCGR step

Full Changelog: 6.1.0...6.1.1

Release 6.1.0

This is a medium release :

• General
  • a new tool called the GenPipes wizard is now available. Perfect for those new to GenPipes, the wizard is an interactive tool that helps users to choose the appropriate pipeline for their data and even builds the correct GenPipes command. Try it out by running:
    genpipes tools wizard
  • cluster-specific config files have been updated to reflect the new clusters available from the Digital Research Alliance of Canada
• AmpliconSeq
  • fixed a small bug that improperly set trimming parameters in some cases
• ChIPSeq
  • metrics changes made in v5.1.0 that were accidentally rolled back in v6.0.0 have been added back to the chipseq protocol
• LongRead DNASeq
  • a new protocol for analyzing matched tumor-normal samples called nanopore_paired_somatic is now available
  • the nanopore protocol of this pipeline has been updated substantially with additional variant calling, structural variant calling, and phased results
• RNASeq
  • outputs for variant calling steps are now organized in their own directory, instead of being added to the alignment directory as before

Release 6.0.0

Version 6.0.0