Anders Sune Pedersen

> Excuse me, I introduce the option --skip_tools haplotypecaller_filter and I can skip the error. The pipeline finished correctly. However, I have a doubt: If we introduce this parameter to...

Similar [issue](https://github.com/nf-core/eager/issues/894) was reported for nf-core/eager. I've occasionally experienced issues with having the pipelines fetch the containers. This problem might also be related to the pipeline fetching or creating containers....

> or we could rename patient to entity? Yeah, "entity" might be better. I was a bit puzzled by the choice of the column name "patient", since the sample doesn't...

I failed at reproducing the error. I ran ``` gatk --java-options "-Xmx5324M" CalculateContamination \ --input sample2.mutect2.pileups.table \ --output sample2.mutect2.contamination.table \ --tmp-dir . \ -tumor-segmentation sample2.mutect2.segmentation.table ``` with `sample2.mutect2.pileups.table` unsorted like...

Hmmm 🤔 So on the abovementioned table strelka is called "Strelka2", but one is suppose to write `--tools strelka` on the command line? Similarly, the command for "GATK Haplotypecaller" is...

I ran this test ``` nextflow run main.nf -profile test,docker --outdir results ``` The only uncompressed vcf-file I could find in the outdir was `results/annotate_mt/justhusky_vep_vcfanno_hmtnote_mt_annotated.vcf`. It turns out that currently...

I found these files which are a bit large and can be compressed: ``` results/qc_bam/*.d4 results/qc_bam/*.wig results/qc_bam/*.bw ``` Should I try to have them compressed?

okay, well, then I can't find any output-files from the raredisease-pipeline that needs to be compressed. Do you know of any?

I think that neither vcfanno nor svdb-query can output compressed VCF-files. Brent of vcfanno suggested just piping to compressor tool: https://github.com/brentp/vcfanno/issues/66

I'm not sure that is the right way to go. (I get the impression that nf-core likes modules to do just one thing, but I could be wrong.) As far...