ENCODE-DCC/atac-seq-pipeline: v1.6.0.1

Conda users need to re-install pipeline's Conda env. $ bash scripts/uninstall_conda_env.sh $ bash scripts/install_conda_env.sh Output file name change (issue #197) Pooled TAG-ALIGN file will have a fixed prefix of rep.pooled instead of using rep1's prefix. Change in default parameters atac.filter_picard_java_heap: 4G to dynamic (atac.filter_mem_mb) atac.preseq_picard_java_heap: 6G to dynamic (atac.preseq_mem_mb) atac.fraglen_stat_pe_java_heap: 6G to 8G atac.gc_bias_picard_java_heap: 6G to 10G Troubleshooting for failed pipelines Added some help texts for stringent IDR threshold Added important GNU apps to Conda env (issue #180) tar: to sort by filename tar --sort grep: to use Perl style regular expression grep -P Misc. Downgraded Java version 11 -> 8 in docker/singularity images. Output def JSON file for Croo: v3 released. bowtie2 log is directly printed to STDOUT instead of printing to .align.lo