seq2science

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows.

• MA plot, volcano plot, and PCA plots added to QC report for deseq2 related workflows

• updated salmon & tximeta versions
• colors for DESeq2 distance plots "fixed"
• updated bwa-mem2 version and reduced the expected memory usage of bwa-mem2 to 40GB
• seq2science now uses snakemake-minimal

• stranded bigwigs are no longer inverted (forward containing reverse reads and vice-versa).
• fix in rename_sample preventing the inversion of R1 and R2 FASTQs.
• bug with parsing cli for explanations
• show/hide buttons for treps are actually made for multiqc report
• fixes in deseq2/utils.R
  • the samples.tsv will now work with only 2 columns
  • the samples.tsv column names will be stripped of excess whitespace, similar to the config.
• ATAC-seq pipeline removing the final bams, keeping the unsorted one