oncoanalyser
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nf-core
A comprehensive cancer DNA/RNA analysis and reporting pipeline
### Description of the bug When I run the nf-core/oncoanalyser, I got the error about work-dir=null for STAR and FASP. So I add the folllowing lines to the modules.config. But...
### 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...
Move the fastp arguments that turn off the adapter/read trimming into the `modules.config` instead of hardcoded into the module itself.
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...