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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