v1.9.5

v1.9.5

What's Changed Across v1.9

• v1.9.5:
  • Adding functionality to check and enforce that Snakemake and Singularity are in the user's $PATH.
  • Updating usage of download_dme_files to include a list of important env variables to export and fixing bug related to variable expansion
• v1.9.4: Updating fastqc rules due to a potential gpfs filesystem issue to use local disk for the temp directory
• v1.9.3: Sort bam files using samtools in single-end rules, avoids a ulimit issue with STAR, samtools is also faster/more efficient too
• v1.9.2: Importing json module from standard library, no longer implicitly loaded by Snakemake in newer versions
• v1.9.1: Updating helper script to run rMATS from an RNA-seek output directory

Full Changelog: v1.9.4...v1.9.5

Release v1.9.0

v1.9.0

• Adding a new --prokaryote option to the run subcommand, which uses a set of alignment options optimized for genomes without introns
• Updating documentation to add a reference to resources/clean_gtf.py script, which can be used to convert and clean/patch an annotation (GFF/GTF file) for the build subcommand.

Release v1.2.1

v1.2.1

• Bumping up bbmerge memory allocation to 64G
• First major release of new documentation
• Parent Release v1.2.0 highlights: added new cache sub command to create local cache on the filesystem for remote resources hosted on - DockerHub
• Added patch to build sub command to include Dockerhub URIs to build config file