A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi <!here>, oncoanalyser 3.0.0 has been released, headline changes include:

_Sequencing data_
Support Ultima and Roche SBX / Axelios sequencing platforms
New UMI processing via fastq-tools
Predefined UMI configuration for selected panels

_Analysis_
Germline amplification calling
ORANGE adjusted for driver reportability changes
Improved noise detection and filtering, and purity fitting in tumor-only mode
Single-step RNA alignment for each sample
Read group overrides in the samplesheet

_New components_
MultiQC for aggregated QC reporting
<https://github.com/hartwigmedical/hmftools/tree/qsee-v1.0/qsee#qsee|QSEE> for detailed per-sample QC reporting with HMF cohort background
<https://github.com/hartwigmedical/hmftools/tree/sage-v5.0.2/sage#variant-visualisations|SAGE visualiser> for per-variant read support HTML reports

_Other_
Migrated to strict Nextflow syntax, workflow outputs, and channel topics

Please see the oncoanalyser <https://github.com/nf-core/oncoanalyser/blob/3.0.0/CHANGELOG.md|CHANGELOG.md> and <https://github.com/nf-core/oncoanalyser/releases/tag/3.0.0|Release Notes> for general details, and also the Hartwig <https://github.com/hartwigmedical/hmftools/blob/e6ba4f2/pipeline/docs/v3_0/WiGiTs_v3.0_ReleaseNotes.pdf|WiGiTs_v3.0_ReleaseNotes.pdf Release Notes> for the specific technical tooling changes

The Hartwig team have also recently developed a detailed and helpful <https://github.com/hartwigmedical/hmftools/blob/e7b47dd/orange/docs/orange_user_manual.pdf|ORANGE User Manual> for navigating, understanding, and interpreting results / findings. It's very well put together and worth reading for new and experienced users alike

Thanks to everyone involved in this release and always special thanks to all the Hartwig folks for the immense amount of work done across their software suite and contributions to oncoanalyser

Hi <@U02JWMPQ23S>, congrats on 3.0.0! What a feat. Quick questions: are there any public slides or recordings for the release? I'm curious to learn about the changes to driver gene panel and various tools parameters. Would be great to learn about the lessons since previous release

Hm. I do like the idea of taking the change log and turning that into slides with some more background information. Matter of finding the time and quizzing all contributors.

Hi <@U0AR5K4EBV5>, thank you, it's been a huge team effort, most congrats of course going to the Hartwig team :)

Interesting idea, and while we don't have any videos, the closest to what you're after would be the technical release notes from Hartwig and their ORANGE user guide, which has further notes re the driver gene panel

On the more instructive side, I'm putting together a set of vignettes that are teaching / learning oriented focused on user stories, including one on customising reference data like the driver gene panel

If you're interested in this, I may ping you for feedback on these

<@U02JWMPQ23S> yes feel free to ping me - it sounds like it would be really useful. I went through the tech release note and was just curious of the parameter adjustments. I'm sure the Hartwig team probably learned a few things with larger cohort, so I was just curious