Skip to content

CHANGELOG.md

Latest commit

 

History

History
43 lines (35 loc) · 2.19 KB

CHANGELOG.md

File metadata and controls

43 lines (35 loc) · 2.19 KB
Raw

Changelog

[v1.8.6]

  • Fix bugs originated after the workflow simplification.

[v1.8.5]

  • Upkeep release.

[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