pipeline-guidelisted

# ENCODE Pipeline Guide and Custom Workflow Generation ## When to Use - User wants to understand ENCODE uniform analysis pipelines or run them on their own data - User asks about "ENCODE pipeline", "Nextflow", "WDL", "processing standards", or "pipeline requirements" - User needs to generate a custom Nextflow/WDL workflow based on ENCODE pipeline specifications - User wants to know compute requirements (CPU, GPU, memory, storage) for running pipelines - Example queries: "how do I run the ENCODE ChIP-seq pipeline?", "what are the compute requirements for Hi-C processing?", "generate a Nextflow pipeline for my ATAC-seq data" Understand ENCODE pipelines, generate user-specific workflows in Nextflow/WDL, and manage compute resources for local, HPC, and cloud execution. ## ENCODE Uniform Analysis Pipelines ENCODE uses standardized pipelines for each assay type, ensuring reproducibility across all datasets. All pipelines are: - **Open source**: GitHub (github.com/ENCODE-DCC) - **Containerized**: Docker and Singularity images - **Written in WDL**: Workflow Description Language (Cromwell execution engine) - **Portable**: Local, HPC (SLURM, SGE, PBS), or cloud (Google Cloud, AWS, Azure) ### Pipeline Repository Map | Assay | GitHub Repository | Primary Tools | Container | |-------|------------------|---------------|-----------| | ChIP-seq | `ENCODE-DCC/chip-seq-pipeline2` | BWA, MACS2, IDR | `encodedcc/chip-seq-pipeline:v2.2.1` | | ATAC-seq | `ENCODE-DCC/atac-seq-pipeline` | Bow