Hugo Tavares

generalise `simulateAlleleFreq()` function to any ploidy

4

In #5 I asked about the `bulkSize` option in `runQTLseqAnalysis()` if: >is it the case that this parameter should be the number of genome copies pooled, which for a diploid...

Contrasts for imbalanced and partially crossed designs

1

I wonder if the strategy I'm using in the tutorial is actually suitable for imbalanced designs. For example, let's say I had 3 replicates in one batch and 6 replicates...

### Description of the bug In the current `dev` branch the modules `MOSDEPTH_AMPLICON` and `PLOT_MOSDEPTH_REGIONS_AMPLICON` seem to be always skipped. This may be related to [these changes](https://github.com/nf-core/viralrecon/commit/eb7a82db49ec338079986c1467d1feeaaac7531d). I'm sorry, I'm...

Allow skipping `freyja boot`

1

### Description of feature To save some computation, it may sometimes be desirable to skip `freyja`'s bootstrapping step. My suggestion would be to allow using `--freyja_repeats 0`. At the moment,...

Clarify documentation on variants tables (inconsistent between platforms)

1

### Description of feature I was trying to understand what variants are included in the `variants_long_table.csv` file, and it seems that this is different depending on the sub-workflow used: -...

I've recently realised that if two objects have different rownames, `cbind()` does not seem to throw an error. Whereas `rbind()` does throws an error if colnames are different (the behaviour...

accessor for "sets/experiments" for easier piping

7

Related to #194 If you decide to use "sets" to refer to experiments within QFeatures, would you then consider creating something like a `sets()` function (in effect just a synonym...