Stephen Watts comments

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                                            Stephen Watts

Implement Neo subworkflow

Force pushing after rebase on top of `alignment-subworkflow`

Implement Neo subworkflow

Descoping from the 1.0.0 release. /cc @charlesshale

Implement Neo subworkflow

Rolling this feature in with feature block one - I've rebased changes on top of `features-block-one-preview` and integrated as needed, now force pushing.

Set bwa-mem2 batch size for reproducibility

I've undertaken a brief investigation of the impact that batch size has on output BAMs to better understand the need to set a consistent batch size (i.e. applying the `-K`...

Set bwa-mem2 batch size for reproducibility

Thanks @maxulysse, I'll take a look at doing this next week. We're using a fairly different approach to sorting/compressing and read group assignment, and the nf-core bwa-mem2/mem module would need...

Move fastp arguments to modules.config

This change makes sense within the nf-core framework wrt use of process selectors to define arguments. I have to admit I'm not much of an advocate for the heavy use...

Move fastp arguments to modules.config

Further rationale for this change: https://github.com/nf-core/oncoanalyser/commit/ba241d1daae37018d4270cac28693f1445448a7f#commitcomment-149188254

Move fastp arguments to modules.config

Good catch, I'll make that change and then merge! That's right we don't perform trimming as it's assumed to have already been done. I'd like to leave the ability for...

Update bwa-mem2 to LLVM

@BiocondaBot please fetch artifacts

Update bwa-mem2 to LLVM

@BiocondaBot please fetch artifacts