Added
- Use profile to determine total elapsed time
- `logging` functions directly on `PipelineManager`
- Re-export `add_logging_options` from `logmuse`, for direct use by a pipeline author.
- `logger_via_cli` that defaults to the `strict=False` behavior of the same-named function from `logmuse`
- Use logging for pypiper-generated output.
Fixed
- Fix childless processes memory monitoring issue
- Fix problems with runtime reading from pipeline profile TSV formatted according to two styles
- Fix problems running containerized executables that would sometimes hang
- Fix inaccurate elapsed time accumulation
- Fixed a bug that caused hanging when running in singularity containerized executables
- Fixed bugs with merging bamfiles using samtools
Changed
- The hashes in the pipeline profile are produced from the entire original command, even if it is a pipe
- Changed output to simplify and improve log readability