Celescope

- Fix numpy version==1.26.0.
- Bugfix: Wrong delimiter results in empty filter_contig.fasta.
- When some read lengths in R1 read are shorter than required, no error is reported.
- Add support for `rna_5p3p`.

`rna` and `dynaseq`
- Adjust the denominator of `Reads Assigned To {Exonic, Intronic, Intergenic, Antisense} regions` from valid reads to mapped reads. This way Exonic + Intronic + Intergenic + Antisense = 100%

General improvments
- Bug fix: Introns was added to gtf when running `celescope utils mkgtf`. Otherwise the featureCounts step will report an error for not finding intron regions.
- Removed the --gzip argument.

General improvments
- Add support for legacy chemistry `scopeV1`.

- Add a new panel `CHIP`.
- Merge all overlapping regions in bed files. Fix KRAS gene in lung_1.bed.

General improvments
- Fix a bug in parsing matrix files from `matched_dir`.

`tag`, `citeseq` and `sweetseq`
- Remove cutadapt from steps.

`citeseq`
- Remove low expression antibody from HTML Umap plot.