v1.1.6.1

Minor release

• Conda users need to update conda environment with the following command line:

$ bash conda/update_conda_env.sh

• bug fixes
  • update incorrectly-built conda package.
  • workaround for cromwell-38 wom API bug (broadinstitute/cromwell#4659)
  • fix for singularity backend hanging problem. use built-in background processing in cromwell instead of & echo $! to print PID.
  • allow irregular chr names in *.hammock.gz (used for Wash U genome browser).
  • fix grep bug in encode_trim_fastq.py

    Traceback (most recent call last):
      File "/software/chip-seq-pipeline/src/encode_trim_fastq.py", line 64, in <module>
        main()
      File "/software/chip-seq-pipeline/src/encode_trim_fastq.py", line 55, in main
        trimmed = trim_fastq(args.fastq, args.trim_bp, args.out_dir)
      File "/software/chip-seq-pipeline/src/encode_trim_fastq.py", line 42, in trim_fastq
        if int(run_shell_cmd(cmd2))>0:
      File "/software/chip-seq-pipeline/src/encode_common.py", line 252, in run_shell_cmd
        raise Exception(err_str)
    Exception: PID=18, PGID=18, RC=1
    STDERR=
    STDOUT=0