Merge pull request #339 from maxplanck-ie/ksikora_release_notes

Ksikora release notes

docs/content/News.rst

@@ -7,11 +7,22 @@ snakePipes 1.1.0
 **26.11.18**
 
  * A wide number of bug fixes to scRNA-seq and other pipelines. In particular, many memory limits were updated.
- * RaceID can be skipped in the scRNA-seq workflow.
  * 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).
 
 snakePipes 1.0.0 (king cobra) released
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