Changelog

[v1.8.4]

Fix broken anaconda environment creation due to wrong repository order
Better schema file
Report generation is now optional and enabled with --report
Report now working with anaconda runs

[v1.8.3]

Added --haplotypes mode, that allows to create liftover files between haplotypes of the same individual with UCSC naming convention

[v1.8.2]

--aligner minimap2 now runs on individual target sequences to reduce the memory footprint and improve performances in large distributed systems
updated dependencies (minimap2 v2.26.0, last v1454, crossmap v0.6.4, bedtools v2.31.0, lastz v1.04.22, blat v445)
fix bug in creating report using singularity/docker images
better lastz management of the input files

[v1.8.1]

Now --source/--target have to be used to pass local, remote or accession IDs (GCAs, GCFs and iGenomes alike)
--ncbi_source, --ncbi_target, --igenomes_source and --igenomes_target now have to be specified alongside --source/--target to tell nf-LO when the files are from the two databases, but do not need any input.
Documentation updated to reflect the change

[v1.7.0]

fix bug aforementioned preventing the lastz alignment of small source contigs or small fragmented source genomes
add support to mamba through the --mamba flag
updated minimal version of nextflow to 21.10.6 in order to support the mamba installation of dependencies
added a new anaconda environment for mafTools
added the possibility of providing custom conservation scores with the --qscores option, followed by the appropriate Q-score file

[v1.5.1]

Lastz has now two extra pre-configurations (primate and general) based on the ensembl pairwise genome alignments parameters
chainNet is now split into three submodules (netChain, netSynt and chainsubset)
There are now three ways to define the source genome (--source, --ncbi_source and --igenome_source)
Similarly, there are now three ways to define the target genome (--target, --ncbi_target and --igenome_target)
Fixed several bugs and stability issues

[v1.5.0]

Initial tagged version