Anders Sune Pedersen

Which branch was this error observed on? Is there a simple test nf-cmd to trigger the error?

That is at least a bug in the [docs](https://github.com/nf-core/rnavar/blob/222d7a15f7f52ff6ce85d0dabb0f3025370690df/docs/usage.md?plain=1#L170). Until it has been fixed, I suggest that using the nf-core pipeline, Sarek, for downloading the snpeff-cache and vep-cache.

Seems to work fine if I drop `--save_output_as_bam`, that is, it works for ``` nextflow run nf-core/sarek -profile test,alignment_to_fastq,docker -r 3.4.2 --outdir results --save_mapped ```

Something wrong here :-/ The test ``` nextflow run main.nf -profile test,alignment_from_fastq_and_spring,docker --outdir results -resume --save_mapped --save_output_as_bam ``` results in bam and bai in different subfolders: ``` results/preprocessing/mapped/test/test-test_L1.sorted.bam.bai results/preprocessing/mapped/test-test_L1/test-test_L1.sorted.bam ```...

> Something wrong here :-/ > > The test > > ``` > nextflow run main.nf -profile test,alignment_from_fastq_and_spring,docker --outdir results -resume --save_mapped --save_output_as_bam > ``` > > results in bam...

> I think publishing should be disabled by default. It bloats the output directory massively and likely folks don't need the converted fastq files in most cases Ok. I'll try...

Do you need to update the changelog for this PR?

@FriederikeHanssen : You mentioned that "GenomicsDB doesn’t work without [intervals](https://nfcore.slack.com/archives/CGFUX04HZ/p1697021746789279?thread_ts=1697021363.120009&cid=CGFUX04HZ )." In connection to that, I feel like pointing out that we now have two subworkflows for joint-germline variant-calling :...

> yes of course, just for the one that uses the genomicsdb route we want to have an early fail Should I add a pytest for that as mentioned above?

Hi @C2i-PeterChung. I would suggest that you come on over on [Slack](https://nfcore.slack.com/channels/sarek) and discuss this problem with us. Did you manage to get the profiles `test` and `test_full` running on...