v1.8.6

This release fixes:

1. blat using the wrong ooc file in some preset, causing the workflow to crash
2. The workflow logging too many times that the user chose a wrong preset

v1.8.5

Maintenance release. Remove duplicated processes, simplify the workflow and better code linting.

v1.8.4

Changes introduced:

• 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

Release 1.8.3

What's Changed

• Support haplotype-resolved liftovers with --haplotypes.

Release 1.8.2

Changes to the workflow

• --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

Release 1.8.0

This version changes the way nf-LO accepts remote input files.

Release notes:

1. Now --source/--target have to be used to pass local, remote or accession IDs (GCAs, GCFs and iGenomes alike)
2. --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.
3. Documentation updated to reflect the change.

Release v1.7.0

This release fixes a major bug preventing the alignments with lastz of the source's small contigs (if large genome), particularly relevant for small, fragmented genomes. It also introduces additional minor changes, workflow customization options, and optimization of the environments.

If affected by the bug, we recommend to discard the older workflow version (<1.7.0) using nextflow drop evotools/nf-LO and rerun the analyses with the newer release.

Release notes:

1. Fix bug aforementioned preventing the lastz alignment of small source contigs or small fragmented source genomes
2. Add support to mamba through the --mamba flag
3. Updated minimal version of nextflow to 21.10.6 in order to support the mamba installation of dependencies
4. Added a new anaconda environment for mafTools
5. Added the possibility of providing custom conservation scores with the --qscores option, followed by the appropriate Q-score file

Stability and usability improvements

This release doesn't add any functionality, but improves the stability and usability of the workflow in general.
A summary of some of the changes done to the workflow:

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

Update configurations for small servers

1.5.0a

Add configuration for very small servers