1.3.1

• Fixed compatibility with snakeMake 5.7.0

1.3.0

• Overhauled WGBS pipeline
• Standardized options to be camelCase
• Further standardized options between pipelines
• UMI handling is now available in most pipelines
• The --fromBAM option is now available and documented
• Users can now change the read number indicator ("_R1" and "_R2" by default) as well as the fastq file extension on the command line.
• Added the preprocessing pipeline, prevented python packages in users' home directories from inadvertently being used.
• Added a snakePipes config command that can be used in lieu of editing defaults.yaml

Release_1.2.3

• Updated citation for snakePipes
• Fixed replicate check for samples with trailing spaces in names
• Fixed input filtering in CSAW
• Several allele-specific RNAseq fixes
• ATACseq peakQC is now run on fragment-size filtered bam
• Fixed Salmon output (Number of Reads output in "*counts.tsv" files and file naming)
• Fixed CSAW QC plot error with single end reads
• Updated histone HMM environment to a working conda version
• Salmon_wasabi is now a localrule

1.2.2

• Fixed a bug in the ATAC-seq environment where GenomeInfoDbData was missing.
• Also an occasional issue with CSAW

1.2.1

• Fixed a typo in createIndices.
• Implemented complex experimental design in RNAseq (differential gene expression), ChIP/ATACseq (differential binding).
• Fixed an issue with ggplot2 and log transformation in RNAseq report Rmd.
• fastqc folder is created and its content will be added to multiqc only if fastqc flag is called.
• fastqc-trimmed folder is created and its content will be added to multiqc only if both fastqc and trim flags are called

1.2.0

• A number of minor bug fixes across all of the pipelines
• Updates of all tool versions and switching to R 3.5.1
• A snakePipes flushOrganisms option was added to remove the default organism YAML files.
• Renamed --notemp to --keepTemp, which should be less confusing

1.1.1

• Fixed some conda environments so they could all be solved in a reasonable amount of time.
• Updated some WGBS memory limits

1.1.0

• A wide number of bug fixes to scRNA-seq and other pipelines. In particular, many memory limits were updated.
• An optional email can be sent upon pipeline completion.
• The RNA-seq pipeline can now produce a fuller report upon completion if you are performing differential expression.
• Sample merging in HiC works properly.
• GTF files are now handled more generically, which means that they no longer need to have "_gencode" and "_ensembl" in their path.
• WGBS: * Merging data from WGBS replicates is now an independent step so that dependent rules don't have to wait for successful completion of single CpG stats but can go ahead instead. * Filtering of differential methylation test results is now subject to two user-modifiable parameters minAbsDiff (default 0.2) and FDR (0.02) stored in defaults.yaml. * Metilene commandline parameters are now available in defaults.yaml. Defaults are used apart from requesting output intervals with any methylation difference (minMethDiff 0). * Additional diagnostic plots are generated - p value distribution before and after BH adjustment as well as a volcano plot. * Automatic reports are generated in every folder containing results of statistical analysis (single CpG stats, metilene DMR stats, user interval aggregate stats), as long as sample sheet is provided. * R sessionInfo() is now printed at the end of the statistical analysis.
• scRNAseq: * An extention to the pipeline now takes the processed csv file from Results folder as input and runs cell filtering with a range of total transcript thresholds using monocle and subsequently runs clustering, produces tsne visualizations, calculates top 2 and top10 markers per cluster and produces heatmap visualizations for these using monocle/seurat. If the skipRaceID flag is set to False (default), all of the above are also executed using RaceID. * Stats reports were implemented for RaceID and Monocle/Seurat so that folders Filtered_cells_RaceID and Filtered_cells_monocle now contain a Stats_report.html. * User can select a metric to maximize during cell filtering (cell_filter_metric, default: gene_universe). * For calculating median GPC, RaceID counts are multiplied by the TPC threshold applied (similar to 'downscaling' in RaceID2).
• all sample sheets now need to have a "name" and a "condition" column, that was not consistent before
  consistent --sampleSheet [FILE] cmdl option to invoke differential analysis mode (RNA-seq, ChIP-seq, ATAC-seq), --DE/--DB were dropped

1.0.0 (King Cobra)

The initial production release, supporting RNA-seq, ChIP-seq, scRNA-seq (Cel-seq2), ATAC-seq and more. Memory requirements have been decreased from the previous beta and alpha releases.

1.0.0-beta2

Various bug fixes, adds the --notemp option to all pipelines. Most importantly, we no longer need to modify snakemake to handle permission issues.