Radically slimmed descendants of the ENCODE processing pipelines (with the custom
allo multimapper-reallocation step), built for efficient peak calling with IDR.
chip-seq-allo-pipeline/— TF/histone ChIP-seq: fastq → trim → bowtie2 → filter → allo → MACS2 (on BAM) → IDR. Controls are pre-built into a common BAM library and sourced lazily. See its README.atac-seq-allo-pipeline/— ATAC-seq (control-free): fastq → trim → bowtie2 → filter → allo (--atac) → ATAC MACS2 cut-site model (on BAM) → IDR. See its README.
Each pipeline is a self-contained Caper/WDL workflow with its own conda envs, cluster submit scripts, and input-JSON generator.