Stephen Watts

Calling groupTuple triggers java.lang.NullPointerException

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## Bug report Under certain conditions calling `groupTuple` appears to trigger a null pointer exception. A MRE is linked below. The process to trigger the null pointer exception in this...

Initial release review [DO NOT MERGE]

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### Background nf-core/oncoanalyser is a cancer DNA/RNA analysis and reporting pipeline that implements the [hmftools workflow](https://github.com/hartwigmedical/hmftools/), which is developed by the Hartwig Medical Foundation. The hmftools workflow provides comprehensive analysis...

MarkDups v1.1.5 may encounter an error processing hard-clipping supplementary alignments when forming consensus sequences. This error can impact users where DNA alignment has been performed outside of oncoanalyser if supplementary...

Implement Neo subworkflow

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I've now rebased this subworkflow on the `alignment-subworkflow` branch since that will be merged soon and includes important changes across the pipeline. (The base branch is also set as `alignment-subworkflow`...

Set bwa-mem2 batch size for reproducibility

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- improve reproducibility for bwa-mem2 alignments by setting `-K` - this ensures that the number of input bases in each batch is consistent - the parameter value was selected to...