v1.2.2

WARNING: Conda users must update their Conda environments.

$ bash conda/update_conda_env.sh

• mixed endedness per replicate. For example of three replicates with mixed endedness. Similarly for controls (ctl_paired_ends).

   {
   	"chip.paired_ends": [false, true, false]
   }

• mixed data type per replicate. For example of three replicates with mixed data type (rep1: BAM, rep2: NODUP_BAM, rep3: TAG-ALIGN). Similarly for controls (ctl_bams, ...).

   {
   	"chip.bams": ["rep1.bam", null, null]
   	"chip.nodup_bams": [null, "rep2.nodup.bam", null]
   	"chip.tas": [null, null, "rep3.tagAlign.gz"]
   }

• no auto-installation for croo/caper inside py3 conda env

• removed resumer support

  • instead, Caper (Cromwell's native call-caching) is recommended

• bug fixes

  • qc_report fails due to type coercion (File -> File?) of outputs from idr/overlap
  • fix for unreplicated pipeline failing on DNAnexus