Release_2.3.0

snakePipes 2.3.0

• Deprecated mode Gruen in scRNAseq.
• scRNAseq mode Alevin now outputs spliced/unspliced counts for RNA velocity estimation based on Soneson et al. 2020, bioRxiv https://doi.org/10.1101/2020.03.13.990069 .
• Fixed "external_gene_name" and "Status" columns in DESeq2 html report.
• Removed warning when sample names start with a number.
• Fixed filtering of empty drops in scRNAseq mode STARsolo.

Release_2.2.3

snakePipes 2.2.3

• Genrich will now run if sampleSheet without replicates is provided.
• Updated zenodo link to mouse genome GRCm38/mm10 .
• Fixed start coordinates in Filtered results bed from CSAW.

Release_2.2.0

snakePipes 2.2.2

• Fix DAG inconsistencies for ChIP-seq and ATAC-seq ran fromBAM and from -d.
• DESeq2 Rmd file is not deleted anymore in noncoding-RNAseq.
• Fixed labels in deepTools commands.
• Allele_info is now boolean.

Release_2.2.1

snakePipes 2.2.1

• Fix a bug in DAG for ChIPseq allelic with CSAW.
• Fixed deepTools qc DAG for ChIPseq with spikein.
• Added DAG test for allelic ChIPseq.
• Fixed a bug with deepTools QC for allelic mRNAseq.

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!

Release_2.1.2

Fixed a bug that was causing noncoding RNA seq workflow fail with SE reads.

2.1.1

• a typo has been fixed in ATAC-seq pipeline which caused a crash in the pipeline.

Release_2.1.0

• Snakemake version is bumped to 5.13.0
• Updated docs on running single snakefiles
• Added user-input target regions and freetext parameters to differential methylation analysis with metilene
• Added PCA to metilene report in WGBS
• Added Genrich support for SE data
• Edited symlinking rules to ln -s or python
• TMPDIR is now passed at rule-level to the shell
• Added logs in a couple of places
• Added --skipBamQC to WGBS to be included with --fromBAM to suppress recalculation of QC metrics on the bam file
• Added tempDir check to snakePipes info
• Added --oldConfig and --configMode options to snakePipes config that allow passing a copy of an existing pre-configured config file instead of passing the single paths. Previous mode can be used with --configMode manual (default), the new mode with --configMode recycle.
• Updated histoneHMM version to 1.8. Changed number formatting in histoneHMM output from scientific to general.
• Small fixes in DESeq2 report for noncoding-RNA-seq, WGBS reports
• Fixed --verbose in WGBS
• Fixed an important bug in differential binding analysis with CSAW (mismatch between sampleSheet rownames and countdata colnames).

Release_2.0.2

A couple of bugs were fixed including:

• Error messages from sample checks interfering with DAG creation
• fastqc with --fromBAM
• WGBS metilene groups and density plots
• HiCExplorer function calls
• outdated commands in zenodo links.

Release_2.0.0

• RNAseq workflow is now called mRNA-seq
• added noncoding-RNA-seq workflow
• added STARsolo mode to scRNA-seq workflow (now default)
• added peak callers to ChIP-seq (Genrich) and ATAC-seq (Genrich and HMMRATAC) workflows
• added results with apeglm-shrunken log2 fold changes to DESeq2 output
• multiple fixes in ATAC-seq, ChIP-seq, RNA-seq, preprocessing and createIndices workflows