clarify changelog

CHANGELOG.md

@@ -3,36 +3,33 @@
 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).
 
-## v3.0.0 - [2023-11-28]
+## v3.0.0 - [2023-11-27]
 
 ### Added
 
-- Add picard CollectInserSizeMetrics to QC workflow [#408](https://github.com/nf-core/rnafusion/pull/408)
-- Build CRAM index in the same directory as CRAM files for arriba and STAR-Fusion [#427](https://github.com/nf-core/rnafusion/pull/427)
+- Add picard CollectInsertSizeMetrics to QC workflow [#408](https://github.com/nf-core/rnafusion/pull/408)
+- Build CRAM index in the same directory as CRAM files for Arriba and STAR-Fusion [#427](https://github.com/nf-core/rnafusion/pull/427)
 
 ### Changed
 
 - Replace PICARD_MARKDUPLICATES with GATK4_MARKDUPLICATES [#409](https://github.com/nf-core/rnafusion/pull/409)
 - Removed `--fusioninspector_filter` and `--fusionreport_filter` in favor of `--tools_cutoff` (default = 1, no filters applied) [#389](https://github.com/nf-core/rnafusion/pull/389)
-- Now publishing convert2bed output to convert2bed to keep the output file for mosdepth [#420](https://github.com/nf-core/rnafusion/pull/420)
+- Now publishing convert2bed output to convert2bed to keep the output file [#420](https://github.com/nf-core/rnafusion/pull/420)
 - No more checks for existence of samplesheet, which made building references fail (building references uses a fake sample sheet if none is provided) [#420](https://github.com/nf-core/rnafusion/pull/420)
-- `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424)
-- `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426)
+- `--annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426)
+- Update vcf creation to get positions/chromosomes and strands even when fusions are filtered out by fusioninspector, using the csv output from fusion-report [#443](https://github.com/nf-core/rnafusion/pull/443)
 - `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429)
 - Change megafusion into vcf_collect, taking into account e.g. the annotation and coding effects outputs from fusioninspector, HGNC ids, frame status... [#414](https://github.com/nf-core/rnafusion/pull/414)
 - CI tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#430](https://github.com/nf-core/rnafusion/pull/430)
 - AWS tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#433](https://github.com/nf-core/rnafusion/pull/433)
-- Update `fusion-report` to 2.1.5p8 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432)
-- Remove `--max_sensitivity --max_mate_dist 10000000` from fusioninspector. Update vcf creation to get positions/chromosomes and strands even when fusions are filtered out by fusioninspector, using the csv output from fusion-report [#443](https://github.com/nf-core/rnafusion/pull/443)
-- Update `fusion-report` to 2.1.8, removing FusionGDB database [#445](https://github.com/nf-core/rnafusion/pull/445)
+- Update `fusion-report` to 2.1.8, updated COSMIC database to fix 404 error, fix download of references via proxy and removing FusionGDB database [#445](https://github.com/nf-core/rnafusion/pull/445)
 - Update documentation [#446](https://github.com/nf-core/rnafusion/pull/446)
 
 ### Fixed
 
 - Fix channel i/o issue in StringTie workflow and add StringTie in github CI tests [#416](https://github.com/nf-core/rnafusion/pull/416)
-- Updated COSMIC database to fix 404 error while downloading fusionreport references [#420](https://github.com/nf-core/rnafusion/pull/420)
 - Update modules, and make sure MultiQC displays the QC results properly [#440](https://github.com/nf-core/rnafusion/pull/440)
-- Add 'when' condition to run collectinsertsize [#444](https://github.com/nf-core/rnafusion/pull/444)
+- Add 'when' condition to run CollectInsertSizeMetrics only when STAR-fusion bam files are available [#444](https://github.com/nf-core/rnafusion/pull/444)
 
 ### Removed