pipeline-wgbslisted

# ENCODE WGBS Pipeline: FASTQ to Methylation Calls ## When to Use - User wants to run a WGBS/bisulfite sequencing pipeline from FASTQ to methylation calls - User asks about "WGBS pipeline", "bisulfite sequencing", "methylation calling", "Bismark", or "bedMethyl" - User needs to process whole-genome bisulfite sequencing data following ENCODE standards - Example queries: "process my WGBS FASTQs", "call methylation levels from bisulfite-seq", "run Bismark on my WGBS data" Execute the ENCODE DNA methylation pipeline for Whole Genome Bisulfite Sequencing data, producing per-CpG methylation levels in bedMethyl format. ## Pipeline Overview ``` FASTQ -> Trim adapters -> Bismark align -> Deduplicate -> sort + index -> MethylDackel -> bedMethyl | | | | | | | FastQC Trim Galore Bismark (Bowtie2) deduplicate_ samtools mbias + coverage bismark extract stats ``` Paired-end only: `TRIM_GALORE` and `BISMARK_ALIGN` both take two mates, and `--reads` must match pairs. ### ENCODE Repository - **GitHub**: `ENCODE-DCC/dna-me-pipeline` - **Container**: built from `scripts/Dockerfile` in this skill (`docker build -t encode-toolkit/pipeline-wgbs:1.0.0 scripts/`); override with `--container` - **WDL**: Available for Cromwell execution - **This skill**: Nextflow DSL2 reimplementation for portability ## Core Tools and Versi