Merge remote-tracking branch 'origin/main' into dev/cutadapt

CHANGELOG.md

@@ -2,16 +2,39 @@
 
 ## BREAKING CHANGES
 
+* Change default `multiple_sep` to `;` (PR #25). This aligns with an upcoming breaking change in
+  Viash 0.9.0 in order to avoid issues with the current default separator `:` unintentionally
+  splitting up certain file paths.
+
 ## NEW FEATURES
 
 * `arriba`: Detect gene fusions from RNA-seq data (PR #1).
 
 * `fastp`: An ultra-fast all-in-one FASTQ preprocessor (PR #3).
 
+* `busco`: 
+    - `busco/busco_run`: Assess genome assembly and annotation completeness with single copy orthologs (PR #6).
+    - `busco/busco_list_datasets`: Lists available busco datasets (PR #18).
+    - `busco/busco_download_datasets`: Download busco datasets (PR #19).
+
+* `featurecounts`: Assign sequence reads to genomic features (PR #11).
+
+* `bgzip`: Add bgzip functionality to compress and decompress files (PR #13).
+
+* `pear`: Paired-end read merger (PR #10).
+
+* `lofreq/call`: Call variants from a BAM file (PR #17).
+
+* `lofreq/indelqual`: Insert indel qualities into BAM file (PR #17).
+
 ## MAJOR CHANGES
 
 ## MINOR CHANGES
 
+* Uniformize component metadata (PR #23).
+
+* Update to Viash 0.8.5 (PR #25).
+
 ## DOCUMENTATION
 
 ## BUG FIXES