Francesco Lescai

I can see that a DEseq analysis has been also extensively discussed in #409 Maybe we could combine all thoughts together? I do agree on the preprocessing: but most likely...

wonderful wonderful! thanks everyone for the hard work on this!!

same here, I must admit. the overhead for some nf-core pipelines is 10X the raw data, which is a lot for our HPC environment.

I would definitely support this. The key logic of nextflow is a little challenged on the cloud: unless one has a shared disk which can be mounted by all tasks...

proposals for docs and changelog updates just submitted. feel free to modify :)

I've added 2 emits for the raw and exported CNV calls. However, at the moment there's no merging of SNP/INDEL variant calls and CNV calls into the variant calling subworkflow(s)....

Hi @achakroun would you be able to share the log file you find in the work folder of your `cnvkit batch` process? I do have all the files you mentioned...

Thanks! I'll have a look and compare as soon as possible. the `cnvkit_reference` is precisely the issue I was meant to address in this fix, as in the current version...