Capcruncher

What's Changed
* fix(packaging): Corrected some install errors
* chore(CI): update CI pipeline by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/269
* feat(pipeline): Improve error reporting by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/270


**Full Changelog**: https://github.com/sims-lab/CapCruncher/compare/v0.3.11...v0.3.12

What's Changed
* chore(packaging): split requirements by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/259
* fix(deps): PuLP<2.8.0 by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/264
* fix: install "full" capcruncher package by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/263
* chore(deps): Bumped minimum capcruncher-tools version by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/262


**Full Changelog**: https://github.com/sims-lab/CapCruncher/compare/v0.3.10...v0.3.11

What's Changed
* Update requirements.txt with latest package by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/252


**Full Changelog**: https://github.com/sims-lab/CapCruncher/compare/v0.3.9...v0.3.10

What's Changed
* build(deps): Update plotly requirement from <=5.17.0,>5.0.0 to >5.0.0,<=5.18.0 by dependabot in https://github.com/sims-lab/CapCruncher/pull/218
* chore: pyarrow minimum to 14.0.1 by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/231
* fix(deduplicate-slices): Wrong Snakemake parameters supplied to script when empty input by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/232
* Fixes UCSC hub generated when create == no by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/230
* CCTrack file_type now accepts all cb tracks by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/229
* fix(report): Use the active kernel for report generation by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/233
* feat(utils): added make_chicago_map cli command by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/228
* Reduce annotation memory usage by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/236
* Feat enable aggregated track plotting by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/235
* chore(deps): pinned polars by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/240
* feat(pileup): added to_pyranges by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/227
* fix(pipeline): using fastqc snakemake wrapper by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/239
* fix(pipeline): Use recursion to format config dictionary by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/242
* fix(ucsc-hub): Correct errors when generating the "Replicates" composite track by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/243
* feat(pipeline): plotting logs moved by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/238
* fix(cis-and-trans-stats): fixes OOM error by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/250
* build(deps): Update pydantic requirement from <2.5.0,>2.4.0 to >2.4.0,<2.6.0 by dependabot in https://github.com/sims-lab/CapCruncher/pull/248
* build(deps): Update pyranges requirement from <=0.0.127 to <=0.0.129 by dependabot in https://github.com/sims-lab/CapCruncher/pull/247


**Full Changelog**: https://github.com/sims-lab/CapCruncher/compare/V0.3.8...v0.3.9

What's Changed
* fix(annotation): Corrects only null values for "get" intersections by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/222
* build(deps): Update pyarrow requirement from <14.0.0,>8.0.0 to >8.0.0,<15.0.0 by dependabot in https://github.com/sims-lab/CapCruncher/pull/216
* chore(CI): Run workflow on PRs by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/225
* Fix to sorting on chromosomes with non-integer names (e.g. 'X') by mtekman in https://github.com/sims-lab/CapCruncher/pull/224
* feat(pipeline): regenerate fastq from capcruncher results by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/226

New Contributors
* mtekman made their first contribution in https://github.com/sims-lab/CapCruncher/pull/224

**Full Changelog**: https://github.com/sims-lab/CapCruncher/compare/v0.3.7...V0.3.8

* Altered the stats report to better include trimming and FLASh stats.
* Updated how statistics are stored for the pipeline run. This should enable greater flexibility to add additional stats later.
* Fixed bug in alignment_filtering causing a freeze in the pipeline. This appears to be an issue with duckdb
* Pinned additional requirements to try and avoid similar errors.
* Additional bug fixes and improvements