bcl2fastq2Pipe

a snakemake based workflow for demultiplexing Illumina runs with bclconvert

automatically does our most-used application, RNASeq analysis with a lot of QC before and after mapping.

For best results, use Ensembl reference genome and annotation!

features

• bclconvert/bcl2fastq2

• interop_plots

• checksum creation

• fastqc, fastp

• cutadapt

• umi_tools

• kraken2

• blastn

• qualimap

• rseqc

• samtools stats, coverage, plot

• stringtie

• prevent weird auto-reverse complement in read 3 if samplesheet created on the wrong Machine

• STAR as main mapper

• 2 multiqc reports: simple + all analysis inclusive

• auto-transfer of folder to other servers

• gocryptfs

• preseq

• sortmerna

  Structure:

  the workflow is actually 3 parts:

  1. demultiplexing, interop plot, checksums of untrimmed data
  2. fastqProcessing: all other parts, excluding
  3. RseQC: only active if rseqc_modules_active= True in config.yaml

Usage:

git pull

edit config.yaml

bash runPipeline.sh