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@katsikora katsikora released this 09 Apr 16:17
· 1449 commits to master since this release
2.1.0
e7235ca
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Learn about vigilant mode.
  • 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).
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