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.