v1.5.0

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.

Pooling control

• chip.always_use_pooled_control is now true by default, which means that pipeline always try to pool controls if multiple control replicates are defined. And such pooled control is used for calling peaks on each experiment replicate.

Added control mode

• Added control to chip.pipeline_type.
• Now chip.pipeline_type has three choices tf, histone and control.
• For control mode, do not use inputs prefixed with ctl_*. Instead, define inputs in non-ctl variables. e.g. define control FASTQs in chip.fastqs_rep1_R1 (not in chip.ctl_fastqs_rep1_R1).

Bug fixes

• Clip peak's genome coordinate between 0 and chromSize.
  • Affected files: SPP/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.