John M. Ma

Remove np.matrix dependency

1

As most of us may know, `numpy` is slowly deprecating the `np.matrix` class. However, the package still has one dependency on this class in `report_matrix.ipynb`, and `scikit-learn` is also in...

This fixes #28 by checking if the module names returned from `.valid_fastqc_modules()` are actually in the `qc` object.

After FastQC version 0.11.6, kmer content is no longer being reported, see https://github.com/s-andrews/FastQC/releases/tag/v0.11.6. However, when we run `qc_plot` with `modules='all'`, the results from `.valid_fastqc_modules(modules='all')` will still contain (`"Kmer Content"`, despite...

I realized one thing: currently, `to_Seurat` will always write the expression to the assay of `'RNA'`. I wonder if devs may add an option so that we can customize the...

splitFastq does not split beyond the second file in PE mode

2

## Bug report (Please follow this template replacing the text between parentheses with the requested information) ### Expected behavior and actual behavior The current Nextflow docs for `splitFastq` states: >Finally...