Maxime U Garcia

Results from the AWS megatests: https://nf-co.re/sarek/results#sarek/results-c87f4eb694a7183e4f99c70fca0f1d4e91750b33/somatic_test/variant_calling/controlfreec/HCC1395T_vs_HCC1395N/HCC1395T_vs_HCC1395N_BAF.png So definitively we can reproduce. Thanks @apeltzer

sorry, this is an ongoing PR, I should have put it as a draft

sorry still need to fix `tumor_normal_pair` test

> @maxulysse What still remains to be done on this PR? This is a pretty substantial bit of refactoring, and I think it would be good to get this merged...

> LGTM. However, we still need to fix the runOptions/containerOptions-issue so that the pipeline can run over awsbatch. We do have a fix for that but it isn't great: >...

Let's keep that aside, until we update the default needed Nextflow version, and probably wait for a newly released version of the plugin as well

> LGTM!! Waiting for a tools release

> The function ascat.aspcf() (found in the [ascat module](https://github.com/nf-core/sarek/blob/3.4.1/modules/nf-core/ascat/main.nf)) accepts a parameter penalty which controls the sensitivity of the tool to potential segment breakpoints. The default is 70 which is...

Hi @C2i-PeterChung, I'm afraid the latest version of Docker has some issues dealing with biocontainers. Can you either try a less recent version, or singularity instead?

That sounds like some credentials issue with AWS, Can you try to unset your AWS credentials prior running the analysis and it should be fine. Otherwise, adding this to a...