ENCODE-DCC/atac-seq-pipeline: v1.8.0

Upgraded WDL to 1.0 Added metadata to WDL Removed hacky comments for Caper. meta for general metadata for pipeline (e.g. version, docker image) parameter_meta for input parameters. Bug fixes Clip peak's genome coordinate between 0 and chromSize. Affected files: MACS2 peak and IDR/IDR_unthresholded/overlap peak. Updated reference genome data hg38: v1 -> v3 mm10: v1 -> v3 No update for old genome data: mm9, hg19. They are still at v1. Reference genome dataset v3: ENCODE4 standard for ATAC/ChIP. New TSS regions (tss) based on GENCODE annotation. hg38: GENCODE v29 mm10: GENCODE vM21 Repacked other annotation BED files: no changes in actual contents. Enhancer (enh) Promoter (prom) DHS regions (dnase) New blacklist (blacklist) for hg38. Keep using old blacklist for mm10