Anders Sune Pedersen

> Do we want to annotate these vcfs on plus the regular ones or instead? I don't know. Right now I'm concatenating the un-annotated, germline vcf-files, and the resulting vcf-file...

> Let's annotate as we are doing for now, we'll add annotating concatenated vcfs in a future PR. Yeah, I'd also say let's just keep this as simple as possible...

Damn! All the hard work I did with getting the variant-callers to return index-files all the way back to `sarek.nf` seems to be redundant, as I'll have to compute new...

Ok, so I introduced a local module for adding the `INFO`-field `SOURCE=`. Here is the concatenated vcf-file [testN.germline.vcf.gz](https://github.com/nf-core/sarek/files/10136598/testN.germline.vcf.gz) With the CLI-options `--concatenate_vcfs` germline-vcf-files from the following variant-callers will be concatenated:...

I'm still passing the index-files from the variant-caller-modules all the way back to sarek.nf; that is actually not necessary with the usage of the local module. Should I get rid...

> I'm still passing the index-files from the variant-caller-modules all the way back to sarek.nf; that is actually not necessary with the usage of the local module. Should I get...

I can't reproduce the problem.

I can reproduce it on the `master`-branch, but it is just a warning: ``` ╭─ [!] 11 Module Test Warnings ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ ╷ ╷ │ │ Module name │ File...

Is this also a problem with Sarek v3.4.2?

> I am also getting a similar input file name collision error when NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES is called: > > `Aug-08 16:16:14.925 [Actor Thread 456] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for...