v1.3.2

IMPORTANT: Conda users must update pipeline's Conda environment (not a re-installation). This will just update pipeline's python task wrappers.

$ bash scripts/update_conda_env.sh

New feature

• Removed a parameter chip.keep_irregular_chr from the pipeline.
• Added a genome-specific parameter regex_bfilt_peak_chr_name instead (chr[\dXY]+ by default, which means chr1, chr2, ... , chrX and chrY). You can define this either in a genome TSV (e.g. keep_irregular_chr[TAB]chr[\dXY]) or in your input JSON (e.g. `"chip.keep_irregular_chr": "chr[\dXY]+") .
  • This parameter defines chromosomes to keep in the final (with .bfilt. suffix) peaks file. This filter is applied even without a blacklist.

Bug fixes

• Pipeline can catch non-zero error code correctly at failed tasks (tasks align and call_peak).
• Pipeline can run without a blacklist.

Dependencies

• Added wget and curl to Conda environment.

Genome data

• Genome database builder generates md5sum-same TAR balls.
• Can use gzipped Bowtie2/BWA indices (.tar.gz) with arbitrary filenames.
  • Files in a TAR ball don't need to be prefixed with TAR ball's filename prefix.