1.3.0 - Antipodean Opaleye

[1.3.0] - Antipodean Opaleye - [2024-08-23]

Enhancements & fixes

• Combined steps to improve the efficiency of the pipeline, especially on large genomes
• "crumble" is now run on every data type, not just PacBio
• Added options for output format and to turn on/off crumble compression (#107)
• Added fastq as possible input type for PacBio (#106) and Illumina/HiC (#96)
• Disabled running bwa index when no short-read data provided (#100)
• Added support for optional custom SAM header (#95)
• Switch to nf-validation (#99) and further updates for nf-core v2.14 compliance (#98)

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency	Old version	New version
blastn	2.13	2.15
minimap2	2.24	2.28
samtools	1.14 and 1.17	1.20
seqkit		2.8.1
seqtk		1.4

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.

Parameters

Old parameter	New parameter
	'--header'
	'--outfmt'
	'--compression

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.