Stephen Watts
Stephen Watts
## 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...
### 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...
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`...
- 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...
This PR is for the initial release following completion of the community review. For details on the community review, please see: - https://github.com/nf-core/oncoanalyser/pull/29 ## Tasks - [ ] Rerun and...
Overview - in order to assist accessibility to developers documentation on design choices should be made available - this should also include other relevant information such as less used Groovy...
Overview - it may be useful for users to have more complete sequence and alignment QC metrics - first we must determine appetite from nf-core community for this extension -...
Overview - some concern around use of the spread operator has been expressed wrt developer accessibility - where a consensus view is made regarding use of Groovy syntax, the oncoanalyser...
Overview - currently I'm using [bump-my-version](https://callowayproject.github.io/bump-my-version/) to manage project versioning - throughout the nf-core community the `nf-core bump-version` tool is also used - however, `nf-core bump-version` only targets specific files...