Friederike Hanssen

In the samplesheet there is a column called `sample` which is a unique sample name. the `normal-sample` MUTECT2 uses is somewhere encoded in the BAM/CRAM header (which is what we...

Yes, sorry that is waht I mean. The file you five with `--input` that contains all your data. So your input file would look sth like this: ``` patient,sample,status,cram,crai p1,normal-sample,0,file.cram,file.crai...

Hi @petanska ! Unfortunately had to push to fix to the next release. Time caught up with us.

Not sure I understand. When setting `--save_reference` it is intended that the bwa index should be saved. Can you elaborate on the issue?

@Githubguanxudong could you elaborate a bit more? We are trying to tackle this during the hackathon. Which tools did you have in mind? Do you have some papers/examples on which...

Thanks for reporting. Taking a look

Can you send me the log and ideally the terminal output? Was GETPILEUPSUMMARIES run?

I would need the .nextflow.log file please

Hi @msguixe ! Apologies for the delay, I was on vacation, but back now. I put it in my todo list for next week. I am afraid I am busy...

Hey! So trying to track this down. On the previous release 3.0.2 it was run on the full size tests: https://tower.nf/orgs/nf-core/workspaces/AWSmegatests/watch/1VrKQdBhYDJB1G https://nf-co.re/sarek/results#sarek/results-bcd7bf9cb98cddec27bb54fb47ee122c09388c02/somatic_test/variant_calling/mutect2/HCC1395T_vs_HCC1395N/ So I think a reference file might be...