Gregor Sturm

Using a custom yaml loader class

1

It would be nice if I could pass a custom callback function for parsing yaml files. There's already support for the native yaml loader and the OrderedDict yaml loader and...

Fix error when passing a boolean mask

1

When passing a boolean mask to `add_modality` (which is supported according to the type hints) using ```python mask = np.zeros((3000, 3000), dtype="uint8") mask [ 500:-500, 20:-500] = 1 ``` It...

Prettier alternatives

2

Prettier requires a full-blown node installation and is rather slow. Alternatives would be welcome. > Maybe we soon don't need prettier anymore: https://biomejs.dev/ > > It doesn't have yaml support...

checkqc doesn't run for bclconvert

3

### Description of the bug I'm running the exact same flowcell, once with bcl2fastq and once with bclconvert. CheckQC only runs when bcl2fastq is selected as demultiplexer. I'd expect checkQC...

### Description of feature I suggest to add a process that checks Illumina Samplesheets for consistency before starting bclconvert/bcl2fastq. This ensures that errors are caught early with useful error messages...