v2.1.0-beta

• Changes to config file
• Restructuring and tidying rule files
• Adding provisional optional support for the GPU accelerated clara parabricks workflow (star + haplotypecaller instead of hisat2 + freebayes). This is not tested yet.
• small fixes
• specify specific versions in pythonGenomics conda env

What's Changed

• Update pythonGenomics env - specific versions of packages by @sanjaynagi in #90
• Do not require VCFs if doing GSEA and remove VENN by @sanjaynagi in #92
• small fixes to pca + gwss notebooks by @sanjaynagi in #95
• coverage was not saving logs to file by @sanjaynagi in #99
• tidy Snakefile and rule files by @sanjaynagi in #101
• add support for clara parabricks by @sanjaynagi in #102
• add local db support for snpeff and update config names by @sanjaynagi in #100

Full Changelog: v2.0.2...v2.0.3

v2.0.2

• Differential isoform expression now optional
• Fix bugs introduced in 2.0.1 in which .xlsx and .csv metadata input was broken.
• Fix for karyotype plotting notebook

v2.0.1

• There was an error in v2.0.0 in which the exampleconfig.yaml was missing one parameter:

jupyter-book:
   activate: True

• Removed a gtf reference from the .test folder which was a relic

v2.0.0

rna-seq-pop v2 is released!!

The major change in version 2, is that we now use papermill and Jupyter book to build a local webpage to display the results of (the major) analyses. This exploring the resulting data reaaally fun and simple.

Results web books can be found in results/rna-seq-pop-results/

v1.0.5

• We have removed FASTQC and Cutadapt, and replaced them with FastP, which trims and assesses quality in one go.
• Updated some envs and wrappers.

v1.0.4

• implemented FDR control in GSEA script
• Reconfigured configs slightly to make them tidier, changed use of ref to reference.
• updated exampleconfig, v1.0.3 version was not up to date and is misleading.
• More complete and up to date docs

v1.0.3

• Support for single-end reads in #57
• added venn #54 and custom gene list heatmaps #53
• Renamed results folder structure #67
• Add options in config for qc rules #64
• Removed qualimap rule which was unused #64
• gzipped pfam/go files for storage #66

recommend users to use this latest release.

v1.0.0

v1.0.0 is released, to coincide with the bioRxiv preprint.

We add support for variant calling with octopus, as well as adding the gatk rna-seq best practices workflow for preparing bam files - base recalibration.

Internally, we have restructured the rule files, to split alignment and variant calling steps, for readability.

v0.8.0

• VariantsOfInterest - fixed a bug which removes NAs from mean frequency calculation
  - added a heatmap plot of allele frequencies in raw read data
  - added asterisks to VOI plot if there is less than 10 reads covering position
  - added Gste2 119V mutation to exampleMutations.tsv file

• Variant Calling - indels are now filtered out before variant analyses

• config yaml - made some changes to configuration file, including grouping Differential Expression and Variant Analysis sections. Almost everything is now optional and missingess filter can be configured for each analysis separately.

• Karyotypes - KaryoPlots.py script added to plot karyotypes

Full Changelog: v0.7.0...v0.8.0

v0.7.0 Zenodo release

• minor updates and bug fixes
• Removed .gtf requirement for simplicity
• Archived with zenodo for citations