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v.0.4.0 - MultiQC reports, further configuration options, docs

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@sanjaynagi sanjaynagi released this 10 May 17:59
· 581 commits to master since this release

This release adds a number of new features-

  • MultiQC report - integrates all QC statistics from other tools, creating a html document

  • samblaster has replaced picard mark duplicates (primarily to remove restrictions with snakemake wildcard pattern matching, but also for speed)

  • Variant calling and the analyses that follow are now entirely optional, specified in the config.yaml

  • Differential expression .xlsx reports are now named after the dataset name provided in the config.yaml

  • FastQ files no longer have to be named in a given convention - one can fill out the config/fastq.tsv file, to match names of fastq reads to samples, and this option is provided in the config.yaml. The old slightly rigid way of filenaming can still be applied by setting fastq: auto: True

  • Every rule in the workflow is now annotated with a brief description of what it does