Stephen Watts
Stephen Watts
Overview - reference data is currently hosted on Cloudflare R2 - while this meets requirements it is desirable to also have the data added to iGenomes Initial discussions 1. https://github.com/nf-core/oncoanalyser/pull/29#discussion_r1677329605...
Overview - MultiQC is not currently used in oncoanalyser and was intentionally removed at early stages of development - it is now becoming a standard for nf-core pipelines to report...
- nf-validation has been replaced by [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) and should be used instead - nf-core reviewers have also suggested some manual samplesheet validation logic could be offloaded to nf-schema - this...
- nf-core reviewers have suggested the local hmftools modules may be good candidates for nf-core/modules - community interest for hmftools modules being part of nf-core/modules will be gauged and assessed...
## Bug report ### Expected behavior and actual behavior Description and background - foreign file staging via HTTP/S can report successful transfer following connection interruption - under certain conditions this...
- VIRUSBreakend uses grep during [execution](https://github.com/PapenfussLab/gridss/blob/v2.13.2/scripts/virusbreakend#L522) - The BioContainers Docker image only provides BusyBox grep, which has poor performance - Increases runtime by up to ~1 hour from the single...
### Description of feature Validation of input FASTQ files should be improved: - certain unsupported samplesheet FASTQ input rows produce non-descript errors - see here for an example: https://nfcore.slack.com/archives/C04CQ1LK7U1/p1724454431405079 -...
- the initial mechanism to support CRAM input has been to simply [handle under the internal `BAM` filetype](https://github.com/nf-core/oncoanalyser/blame/c3a1d0cfa7c7a2caa853f753f4bf6f82aa9fc975/lib/Utils.groovy#L151) - support for CRAM should be more explicit and be given an...