Andrew Frantz

Also facing this on a cluster with conda-forge dependencies. Seems I can't install new packages in any of my conda environments, even ones without conda-forge.

@ewels Hi Phil. I'm also having trouble with custom content beeswarms. My data is correctly parsed and presented as a table, but it would be much easier to view the...

@ewels Big change in runtime! No change in memory consumption. It went from taking 3 hours to process ~2000 samples (total of ~239000 files to search through) down to only...

Seems to me like there are two serious problem modules (in my set of 9 at least): mosdepth used 51gb memory* and kraken used 37gb. fastqc is also a potential...

First: mosdepth [SJWLM030704_X3.RNA-Seq.MarkDuplicates.CDS.mosdepth.summary.txt](https://github.com/ewels/MultiQC/files/12345130/SJWLM030704_X3.RNA-Seq.MarkDuplicates.CDS.mosdepth.summary.txt) [SJWLM030704_X3.RNA-Seq.MarkDuplicates.CDS.mosdepth.region.dist.txt](https://github.com/ewels/MultiQC/files/12345131/SJWLM030704_X3.RNA-Seq.MarkDuplicates.CDS.mosdepth.region.dist.txt) [SJWLM030043_D1.RNA-Seq.exon.mosdepth.summary.txt](https://github.com/ewels/MultiQC/files/12345132/SJWLM030043_D1.RNA-Seq.exon.mosdepth.summary.txt) [SJWLM030043_D1.RNA-Seq.whole_genome.mosdepth.summary.txt](https://github.com/ewels/MultiQC/files/12345133/SJWLM030043_D1.RNA-Seq.whole_genome.mosdepth.summary.txt) [SJWLM030043_D1.RNA-Seq.exon.mosdepth.region.dist.txt](https://github.com/ewels/MultiQC/files/12345134/SJWLM030043_D1.RNA-Seq.exon.mosdepth.region.dist.txt) [SJWLM030043_D1.RNA-Seq.whole_genome.mosdepth.global.dist.txt](https://github.com/ewels/MultiQC/files/12345135/SJWLM030043_D1.RNA-Seq.whole_genome.mosdepth.global.dist.txt) Attached are the two largest `*dist.txt` files (and accompanying `summary.txt`) and the smallest `*dist.txt` file (and accompanying `summary.txt`) from our RNA-Seq cohort....

Second: kraken2 [SJBALL013327_D1.RNA-Seq.kraken2.txt](https://github.com/ewels/MultiQC/files/12345176/SJBALL013327_D1.RNA-Seq.kraken2.txt) All of our Kraken files are essentially the same size. So attached is just a random report from our RNA-Seq cohort. I assume they're the same size...

@ewels The new `endedness` command (and the old `strandedness` command) support a parameter called `--split-by-rg`. This does what it sounds like it does; instead of one entry per sample (BAM),...

> @a-frantz not really I'm afraid, at least - not yet. I've been wanting to add some core functionality to handle groups of samples / results for years. I actually...

@ewels I'm working on a [v4](https://github.com/stjudecloud/ngsderive/pull/139) release of ngsderive. It involves some breaking changes that will need to be accommodated for in MultiQC*. Would you rather me knock this current...

We've started using the `remove-sections` MultiQC config to streamline our reports (worried about users getting distracted/overwhelmed by data we want to collect but deem "less important" for summary purposes). So...