Summary of changes

• Alternative filtering tool with --filtering_tool bbmap (default as previous versions with seqkit)
• Added peer-reviewed paper as pipeline citation
• Updated nf-core modules software versions
• Updated nf-core template (now 3.4.1)

Detailed changes

Added

• PR #80 - bbmap/filterbyname.sh natively handles pair-end reads, eliminating the steps required to modify fastq headers, improves run time, choose via --filtering_tool bbmap (by @m3hdad)

Changed

• PR #79,PR #87 - Update pipeline version (by @d4straub)
• PR #81 - Update citation from preprint to peer-reviewed publication (by @d4straub)
• PR #84 - Template update for nf-core/tools 3.4.1 (by @d4straub)

Fixed

• PR #90 - Update minimum nextflow version to 25.04.8 to fix conda (by @d4straub)

Dependencies

• PR #86 - Update nf-core modules (by @d4straub)