nf-core/pairgenomealign v2.3.0 – Umi budou

v2.3.0 "Umi budou" - [June 10th 2026]

Added

• New --multi_cram option to produce a multi-query CRAM file combining all the alignments (#60).
• New --multiqc_thumbs option to produce alignment thumbnails in the MultiQC report (#93).
• New --strand option to index only one strand of the genome, which reduces memory usage at the expense of speed, and suppresses -/+ alignments (#97).
• New --query and --queryName convenience options to skip samplesheet creation when there is only one query genome to align (#112).
• In the GFF export format, the target genome sequence lengths are now exported in ##sequence-region fields (#70).

Fixed

• Using the nf-core version of the FASTA_BGZIP_INDEX_DICT_SAMTOOLS subworkflow that we just contributed.
• Check for input file existence in the parameter schema #73).

Parameters

Old parameter	New parameter
	--multi_cram
	--multiqc_thumbs
	--query
	--queryName
	--strand

Dependencies

Dependency	Old version	New version
SAMTOOLS_BGZIP	1.21
SAMTOOLS_DICT	1.21	1.23.1
SAMTOOLS_FAIDX	1.21	1.23.1
SAMTOOLS_MERGE		1.23.1
HTSLIB_BGZIPTABIX		1.23.1