SciLifeLab/scilifelab — pull request #206 by percyfal (2013-03-05 06:59:12+00:00)
Title: Develop - new feature halo_pipeline

Add support for analysis of HaloPlex data. This commit adds a directory 'experimental' for new features that, when deemed stable, should be moved into the main tree before going into the master branch. The current implementation consists of a shell script, 'halo_pipeline.sh', which eventually should be ported to python for easier integration with the rest of the code. The new pm function 'run_halo' is used for submitting an analysis:

pm project run_halo J_Doe_00_01 --drmaa

New functionality includes:

- new module scilifelab.experiment.project that contains functions for finding samples based on directory structure, and not config files as the similar function in scilifelab.bcbio
- add files to best practice data delivery
- add steps to vcf_summary (including merging and indexing with tabix)
- modules, scripts, and config files for HaloPlex analyses