Added support for time-series RNA-Seq experiments by generalising the code around Cuffdiff.
Adjusted the documentation to indicate column names for RNA-Seq time-series experiments.
Fixed the logic in the hierarchy of function calls. First, test for the presence of the result file from a particular function, before eventually delegating to the up-stream function.
Made the use of the string.join method more consistent by always specifying keyword arguments.
Fixed DRMS.dependencies between analysis steps.
Made the use of the string.join method more consistent by always specifying keyword arguments.
Specified the argument for the process_macs14 Executable directly, rather than via the name option of the macs14 Executable.
Adjusted file names, since the GVCF format only applies to the results of the GATK Haplotype Caller and the GATK Combine GVCFs analysis steps.
Activated Intel optimisations in the GATK Haplotype Caller via pair_hmm_implementation.
Assess the completion of an analysis step on a VCF index file where possible, as those a written last.
Used the GATK Variant Annotator step to additionally pull in fields from the GATK Bundle dbsnp resource file.
Adjusted UCSC Track Hub annotation and made hubs more consistent between the ChIP-Seq and RNA-Seq pipelines.
Fixed a format string.
Utilize extend_path of the pkgutil module to allow joining of BSFPython with BioPython, which both use the Bio name space.
Further work on SQLite database support.
The SLURM DRMS module now utilises an SQLite database for tracking SLURM process identifiers in dependencies.
The name of a cohort is now configurable and defaults to just 'default'.
Annotation resources (dbSNP) are now systematically configurable.
Only submit an Executable if the final result file does not exist.
Code cleanup to avoid temporary string objects where they are not required.
In _read_vqsr_configuration raise Exceptions rather than just issue UserWarning objects.
In the Gene Expression Profiles section of the RNA-Seq report provide also links to the BAM and BAI files produced by Tophat.
Refactor the UCSC Genome Browser Track according to Christoph Bock's suggestions.
Removed code redundancy by introducing a new run_executable function.