maxplanck-ie/snakepipes: Release_2.2.0

snakePipes 2.2.0 Added Alevin mode in scRNA workflow Added a new conda environment using to call AlevinQC. Added filtering of empty drops with Dropletutils to scRNA-seq mode STARsolo Added spikein normalization to ChIPseq workflow Added hybrid genome creation to createIndices Added STARsolo report for all samples to STARsolo output folder FASTQ1 and FASTQ2 are not localrules anymore due to buggy logging Included optional differential splicing analysis using rmats within mRNA-seq workflow Symlinks in the output path are relative Increased BBmap version Increased STAR version to 2.7.4a in scRNAseq, noncoding-RNA-seq and mRNA-seq workflows Fixed snakemake version at 5.18.0 due to a bug in DAG handling Minor changes to shared FastQC and multiQC rule with regards to scRNA-seq workflow. Fixed issue with missing input for running the DNA-mapping Snakefile Fixed rule TrimGalore for single end reads deepTools heatmaps for differentially bound regions are now ordered by sample sheet condition Genrich is now run on namesorted bams Workflow help message now points to example sampleSheet on GitHub organismsDir can now be updated with snakePipes config mode "recycle" .. note:: Please be aware that this version requires regeneration of STAR indices