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

dxy, genes2transcripts and small fixes

• The gene_names file is now a Genes to Transcript Map, and contains 4 columns - GeneID, TranscriptID, GeneName, GeneDescription. The last two columns are optional. Previously the workflow would only work with VectorbaseIDs, now gene names can be arbitrary.

• A Per Gene dxy calculation has now been implemented.

• A fix has been implemented for the calculation of inbreeding coefficients.

• The DifferentialSNPs module is now fixed.

v0.5.0 - Haploidy, small fixes

The following fixes and improvements have been made:

• The pipeline can now handle haploids

• the 'samples' column of samples.tsv file has been renamed to 'sampleID', for clarity.

• the samples.tsv file is now referred to as 'metadata' internally, rather than 'samples', for clarity.

• fix bug that occured if IRmutations module is not run.

• scripts now directly read the config for the contrasts, as opposed to previously a separate file was made at the beginning at the pipeline.

• There is now a dedicated discord channel, see README.

v.0.4.0 - MultiQC reports, further configuration options, docs

This release adds a number of new features-

• MultiQC report - integrates all QC statistics from other tools, creating a html document

• samblaster has replaced picard mark duplicates (primarily to remove restrictions with snakemake wildcard pattern matching, but also for speed)

• Variant calling and the analyses that follow are now entirely optional, specified in the config.yaml

• Differential expression .xlsx reports are now named after the dataset name provided in the config.yaml

• FastQ files no longer have to be named in a given convention - one can fill out the config/fastq.tsv file, to match names of fastq reads to samples, and this option is provided in the config.yaml. The old slightly rigid way of filenaming can still be applied by setting fastq: auto: True

• Every rule in the workflow is now annotated with a brief description of what it does

v0.2.0 - karyotype + ag1000gSweeps

This release adds two new modules to the pipeline:

Karyotype - Runs compkaryo to determine inversion status of samples

Ag1000gSweepsDE - Finds DE genes that also sit underneath selective sweeps in the Ag1000g. Reports which sweeps they are found under. Uses Ag1000g phase 1 data for now.

Initial release - RNA-Seq-IR

Continous integration with Travis-CI is now up and running, and I will move to working on a development branch of the repo.