ENCODE-DCC/chip-seq-pipeline2: v1.8.0

Conda users must update pipeline's environment.

$ bash scripts/update_conda_env.sh

Added input parameters:

• chip.bowtie2_use_local_mode
  • If this flag is on then the pipeline will add --local to bowtie2 command line, which will override the default --end-to-end mode of bowtie2.
  • See details in this bowtie2 manual.
• chip.bwa_mem_read_len_limit
  • This parameter is only valid if chip.use_bwa_mem_for_pe and FASTQs are paired-ended.
  • This parameter defaults to 70 (as mentioned in bwa's manual).
  • This parameter controls the threshold for read length of bwa mem for paired ended dataset. The pipeline automatically determines sample's read length from a (merged) FASTQ R1 file. If such read length is shorter than this threshold then pipeline automatically switches back to bwa aln instead of bwa mem. If you FASTQ's read length is < 70 and you still want to use bwa mem then try to reduce this parameter.
  • See details in this bwa manual.

Conda environment

• Added and fixed version of tbb in the environment, which will possibly fix the bowtie2 and mamba conflicting library issue.