v1.3.5

[leepc12]

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

• Pooled TAG-ALIGN file will have a fixed prefix of rep.pooled instead of using rep1's prefix.

Change in default parameters

• chip.filter_picard_java_heap: 4G to dynamic (chip.filter_mem_mb)
• chip.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

• 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.log
• removed wrong arrow (FASTQ R2 -> chip.xcor) in task graph in Croo's HTML report.