Anders Sune Pedersen

> There are some file for which you are testing for content when the md45sums change and for some you aren't. Is there a reason for it? If the md5sum...

> what did you use to run it? Docker? @SusiJo told me she used Docker.

The md5-sum of certain output-files, like the following, keep changing between reruns. ``` test.md.cram test.md.cram.crai test.md.metrics hash_table.cfg hash_table.cfg.bin hash_table_stats.txt ``` The contains something like timestamps or the names of work-directories...

I would also appreciate more detailed per-site info in the output from somalier. Would it perhaps be possible for the `extract`-function, in addition to the `.somalier`-files, to output a TSV-file...

Is anybody actively working on this at the moment?

> Not that I know of. I can close the issue (as long as the raredisease pipeline is concerned, we are happy with local modules). We want to implement Sentieon...

What is the right tool for this? `bcftools concat`? We already have a module for that: https://github.com/nf-core/modules/tree/master/modules/nf-core/bcftools/concat

As far as I could tell, we need to run `bcftools concat` with the option `--allow-overlaps`? https://samtools.github.io/bcftools/bcftools.html If one doesn't use `--allow-overlaps`, the results from `bcftools concat a.vcf b.vcf` and...

I was able to reproduce the issue. The error is raised around [here](https://github.com/nf-core/tools/blob/9eac5e9b33a4b86a5228e950a8c8fd16765f4a85/nf_core/schema.py#L463-L467). Not sure how it should be handled 🤔 @mirpedrol @mashehu @apeltzer : Perhaps the function [check_for_input_mimetype](https://github.com/nf-core/tools/blob/9eac5e9b33a4b86a5228e950a8c8fd16765f4a85/nf_core/schema.py#L449C9-L449C33) can...

Indeed, the `environment.yml-file seems to be missing. It might be that the pipeline has not been very well tested with conda. (It is my impression that very few people use...