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nf-core/pangenome: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

1.2.0dev - marsupial

1.1.2 - canguro

This release reverts the wfmash tool version to 0.10.4, because the current releases are unstable, not documented, and I don't understand how to set the parameters properly. It is currently unclear, when a new stable release will become available. @baozg or @AndreaGuarracino are evaluating.

  • Per default, we set the number of mappings in wfmash to --n_haplotypes - 1. Previously, this was set to 1.
  • Deactivated parameter wfmash_hg_filter_ani_diff, because the older wfmash version does not support it.

1.1.1 - LATÜRNICH

This release fixes some important bugs:

  • Per default, we set the number of mappings in wfmash to 1. Previously, this was set to the given number of haplotypes.
  • To complement the issue above, there is a new parameter wfmash_n_mappings with default 1.
  • bcftools in the VG_DECONSTRUCT module was updated to the most recent version 1.19 to prevent errors like corrupted size vs. prev_size.
  • Fixed some problems with the delimiter in VG_DECONSTRUCT so that the parameters given by --vcf-spec are now applied correctly.
  • Updated to nf-core template version 2.13.1

1.1.0 - Schmuddlweddr

This release mostly contains updates of the respective modules. Functional updates are the following:

  • Added parameter wfmash_hg_filter_ani_diff mirroring pangenome/pggb#351: Filter out mappings unlikely to be this Average Nuclotide Identitiy (ANI) less than the best mapping. The default values is 30.
  • seqwish_min_match_length new default value is 23 now.
  • Fixed a bug with wfmash_exclude_delim where # was interpreted as a comment instead of a string.
  • @heringerp added functionality so that very large integer values can be written in short form: For example 5000 would become 5k.

1.0.0 - Ratzupaltuff

Initial release of nf-core/pangenome, created with the nf-core template.