version 0.1.1

This release includes bug fixes and a new feature, where the annotation files are now also saved into the results folder for backwards compatibility.

version 0.1.0

This is a maintenance release. Most importantly, it fixes a bug when using knitr 1.39.

Full Changelog: v0.0.21...v0.1.0

version 0.0.21

Variety of new sanity checks are added, which are related to checking the sample sheet, settings, and annotation files such as the genome, transcriptome and gene annotations. File contents are also cross-checked to make sure about the compatibility of, for instance, the annotation sources.

version 0.0.20

Updates since version 0.0.19:

• Additional options in the settings file to make the reports more descriptive and debuggable
• Some bug fixes about manipulating count files
• New feature: now megadepth is used as default to compute the genome coverage. Deeptools' bamCoverage is kept as an option.
  This can be configured in the settings file with the parameter setting "coverage->tool".

version 0.0.19

v0.0.19

version bump to 0.0.19

version 0.0.18

• The pipeline now uses a launcher submodule that is common to other pigx pipelines

version 0.0.17

Major changes since version 0.0.13:

• Replaced rtracklayer::export.bw with deeptools::bamCoverage for computing genome coverage profiles. This is supposed to decrease memory consumption and give better flexibility to the user in defining how to compute coverage profiles.
• Added snakemake resources + memory requirements per rule
• Fixed issues #61, #64, #72, #96, #97

version 0.0.13

Major updates since 0.0.10 release:

• Added support to configure the mapper (STAR + HISAT2)
• Clean up intermediate SAM files after sorted BAM files are obtained
• FASTQC and TRIM-GALORE are dropped from the pipeline. Instead a faster package (fastp), which handles
  both read trimming/filtering and quality control reporting is added to the pipeline.
• The updates should increase both the speed (particularly in read filtering), maximum memory
  consumption (when HISAT2 is used) and disk space usage (by removing unused SAM files)

Version 0.0.10

• Improved cluster memory configuration
• Bug fixes:
  • More flexible in sample names
  • ggplot discrete color pallette issue

Version 0.0.9

• More flexibility in naming samples
• better defaults for memory requirements important for cluster submission.
• use sorted BAM Files to compute coverage scores.