Release 2.0.0

This major release adds several features, bug fixes, and changes to the production pipelines.

All Production Pipelines

• Supports Toil's major 3.3.0 release
• This release is pip installable: pip install toil-scripts==2.0.0 ( #260 )
• Pipelines are callable via an entrypoint which displays help menu and run information
• Pipelines are now uniformly run, by generating a YAML configuration file and optional manifest to declutter the command line arguments and disambiguate pipeline-specific arguments from Toil arguments.
• sudo has been deprecated from Docker commands and pipelines ( #282 )
• Pipelines now have continuous integration testing ( #239, #254, #215, #238 )

RNA-seq Pipeline

• STAR/RSEM and Kallisto are now modular (#262)
• Added wiggle output support ( #312 )
• Cores fix — specifying maxCores will propagate to tools ( #300 )
• Removed RSEM post-processing files that had redundant and inaccurate normalization , now returns only RSEM output and normalized counts ( #283 )
• Added FastQC to RNA-seq ( #233 )
• Outputs sorted, indexed, genome-aligned bam from STAR instead of transcriptome bam

Exome Pipeline

• Added Pindel for indel calling ( #276 )
• Added MuSe as an additional variant caller ( #276 )
• GATK Preprocessing, MuSe, Pindel, and MuTect are all optional / modular
• Exome inputs added to Synapse ( #284 )

BWA Alignment Pipeline

• Supports single-end fastq ( #322 )
• Requires only reference instead of all index files ( #320 )
• Uses only BWA-kit now which is faster and simpler ( #225 )

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