Stephen Watts

This is prohibiting regular/routine use of AGC for us as well. Publishing outputs in a specific directory to rename and organise results is a key feature for many NF pipelines...

Thanks for spending the time putting this together. What do you think about removing the Win32 preprocessor guard and dropping any implicit/supposed Windows support entirely?

Thanks for the PR, could you please amend the commit message to be more descriptive (e.g. fix typo in README.md)?

Hi @taijiyamazoe, can you please attach your `nf_sample.csv` samplesheet and also confirm that all files provided in it exist?

No worries! I'm planning to improve samplesheet checking to make it clear when this happens, it's not very obvious at the moment. The required software (e.g. fastp, bwa-mem2, STAR, etc)...

Unfortunately the 0.4.5 version has incomplete Conda support as you've seen. There is better Conda support in the `dev` branch but switching to that from `0.4.5` requires reorganisation of reference...

I'm not surprised you're encountering conflicts trying to create a single Conda environment with all dependencies required, using Docker is a much better approach - glad to hear you've switched!...

I've created issues to continue on-going activities that do not block the initial release: - https://github.com/nf-core/oncoanalyser/issues/50 - https://github.com/nf-core/oncoanalyser/issues/51 - https://github.com/nf-core/oncoanalyser/issues/71 - https://github.com/nf-core/oncoanalyser/issues/79 - https://github.com/nf-core/oncoanalyser/issues/80 - https://github.com/nf-core/oncoanalyser/issues/81 - https://github.com/nf-core/oncoanalyser/issues/82 - https://github.com/nf-core/oncoanalyser/issues/83...

As discussed on the nf-core Slack, all reviewers have given their approval and so we can now conclude the community review. There are several topics additional of discussion / points...

Now closing this PR so I can open the 'Release 1.0.0' PR