Releases: maxplanck-ie/snakepipes
Releases · maxplanck-ie/snakepipes
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
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 -sor python - TMPDIR is now passed at rule-level to the shell
- Added logs in a couple of places
- Added
--skipBamQCto WGBS to be included with--fromBAMto suppress recalculation of QC metrics on the bam file - Added tempDir check to snakePipes info
- Added
--oldConfigand--configModeoptions 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
--verbosein 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