add citations and changelog

Author: kubranarci

CHANGELOG.md

@@ -3,14 +3,37 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0dev - [date]
+## 1.1.0 - [06.03.2025]
 
 Initial release of nf-core/variantbenchmarking, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 
+- CNV benchmarking subworkflow
+- Method: _intersect_ to intersect two regions (BED) files given
+- zenodoid
+- rtgtools vcfeval added for small somatic variant benchmarking
+
 ### `Fixed`
 
+- truth.md links are removed
+
 ### `Dependencies`
 
 ### `Deprecated`
+
+## 1.0.0 - [24.02.2025]
+
+Initial release of full functioning nf-core/variantbenchmarking
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`
+
+## v1.0dev - [12.02.2024]
+
+Initial release of nf-core/variantbenchmarking, created with the [nf-core](https://nf-co.re/) template.

CITATIONS.md

@@ -26,6 +26,10 @@
 
 > Aaron R. Quinlan, Ira M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, Volume 26, Issue 6, March 2010, Pages 841–842, https://doi.org/10.1093/bioinformatics/btq033
 
+- [bedops](https://bedops.readthedocs.io/en/latest/)
+
+> Shane Neph, M. Scott Kuehn, Alex P. Reynolds, Eric Haugen, Robert E. Thurman, Audra K. Johnson, Eric Rynes, Matthew T. Maurano, Jeff Vierstra, Sean Thomas, Richard Sandstrom, Richard Humbert, John A. Stamatoyannopoulos, BEDOPS: high-performance genomic feature operations, Bioinformatics, Volume 28, Issue 14, July 2012, Pages 1919–1920, https://doi.org/10.1093/bioinformatics/bts277
+
 - [datavzrd](https://datavzrd.github.io/docs/index.html)
 
 - [hap.py](https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html)
@@ -50,6 +54,8 @@
 
 - [SVanalyzer](https://svanalyzer.readthedocs.io/en/latest/index.html)
 
+- [svtk](https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk)
+
 - [svync](https://github.com/nvnieuwk/svync)
 
 - [tabix](https://www.htslib.org/doc/tabix.html)