v1.7.0

Conda users must update their environment.

$ bash scripts/update_conda.env.sh

Added chip.redact_nodup_bam

• This will redact filtered/nodup BAMs by replacing indels with reference sequences to protect donor's private information.

Added chip.trimmomatic_phred_score_format

• Choices: [auto (default), phred33, phred66] (no hyphen).
• Users can activate Trimmomatic's flag -phred33 or -phred66 by defining this parameter as phred33 or phred66.
• Defaults to auto (using Trimmomatic's auto detection).
• More details at [this doc] (http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf)

Removed caper and croo from pipeline's Conda environment.

• There has been some conflicts between conda-forge and bioconda packages. These two apps will be added back to the environment later after all conflicts are fixed.