SciLifeLab/scilifelab — pull request #169 by percyfal (2013-02-05 15:43:19+00:00)
Title: Develop v 0.3.0 - new features

This pull request contains many new features which motivates a version bump to 0.3.0. New features include the following:

- add command 'pm project bpreport' to generate best practice reports for sequence capture
- add command 'pm deliver best-practice' for delivering best practice results for sequence capture application
- --phix option now accepts dictionary, so that an error rate can be provided on a per-lane basis
- new option --include_all_samples includes all samples in a project status report. Default is to only include the last library prep
- new option --from_ssheet makes it possible to start analyses from SampleSheet.csv files. Convenient for MiSeq analyses.
- new option --batch allows for submitting several jobs to a single node to be run sequentially. Convenient for e.g. compress operations
- add simple progress indicator for data transfer from production to projects
- make rsync do data transfers
- improve formatting of reports

Bug fixes
- read counts from demultiplex_stats.htm now return lane by lane, and as number read pairs, not number of reads
- miscellaneous clean-up