Harshil Patel

It might be good to host a central database (e.g. yaml) of tools and their associated information. This can then be used to parse the conda yaml to create a...

How about tool-specific parameters? e.g. if you aren't using the defaults. I generally provide these as a double-quoted string for full traceability and reproducibility. Would it be enough to have...

We use the `--broad` setting in MACS2 by default for this pipeline because that tends to be better suited to the variable peaks sizes you have with ATAC-seq data. MACS2...

Hi @Temperche . That sounds like a sensible proposition. It may not be too difficult to add this but I suspect it will take a bit of testing to make...

You could in theory create a dummy `gtf` file with several intervals and give that to the pipeline? Havent tried it before but the worse case scenario is that you...

Hi @Temperche so looking at this in a bit more detail it appears that its going to take quite a bit of work to fully implement and test making the...

Yep, I am seeing a similar thing and was a little confused too but it makes sense now if only the `profile` definitions on `master` are pulled in. In my...

Tests are expected to fail here due to recent breaking changes introduces in the NCBI API. The plan is to try and get the tests passing again using `ffq` instead...

Hi @dmalzl ! Thanks for looking into a fix. Yes, the NCBI changed their APIs yet again with a breaking change. Given this pipelines and other tools make assumptions about...

True origins from rnaseq [here](https://github.com/nf-core/rnaseq/blob/89bf536ce4faa98b4d50a8ec0a0343780bc62e0a/workflows/rnaseq.nf#L202-L222)! Just need to figure out how we report the ids in this case after merging i.e. if this parameter is provided do we name files...