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nf-core/multiplesequencealign: Changelog

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

1.0.0 - Somorrostro

Somorrostro is a beach in Barcelona.

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

Added

  • [#29] - Add FAMSA_ALIGN module.
  • [#38] - Add FAMSA_GUIDETREE module.
  • [#42] - Add MAFFT module.
  • [#51] - Add CLUSTALO module.
  • [#41] - Add KALIGN module.
  • [#48] - Integrate NF-VALIDATION PLUGIN.
  • [#45] - Add module LearnMSA
  • [#35] - Add module Tcoffee_align.
  • [#60] - Add module Tcoffee3D_align and handle structures input.
  • [#35] - Add module MUSCLE5_SUPER5.
  • [#59] - Add support for passing structure template in samplesheet.
  • [#77] - Add module zip.
  • [#93] - Add multiqc basic support. Add custom params validation. Add basic shiny app.
  • [#100] - Add support for optional stats and evals. Clean tests.
  • [#110] - Add Readme documentation. Add nf-test for the pipeline.
  • [#76] - Add reading of trace files for shiny app.
  • [#99] - Add check for conflicting input parameters for stats and eval.
  • [#117] - Add data for full datasets.
  • [#90] - Add TCS evaluation metric.
  • [#89] - Add collection of plddt metrics in stats subworkflow.
  • [#96] - Add collection of number of gaps in eval subworkflow.
  • [#84] - Update Metromap.
  • [#139] - Add Foldmason.
  • [#146] - Only show additional process tags when they exists and use the same ubuntu version in all modules.
  • [#145] - Add consensus MSA.
  • [#147] - Add small testing profile + some fixes of the shiny app.
  • [#148] - Add UPP module.
  • [#150] - Update modules and readme for pre-release.
  • [#174] - Add the chaining of proteinfold output to MSA input.

Fixed

  • [#61] - Fix filtering of unique guidetree compuation instructions: no double GT computation.
  • [#57] - Update naming in the naming of the meta channels.
  • [#66] - README: add new metromap and available tool list.
  • [#54] - Update modules versions from nf-core tools.
  • [#80] - Update modules versions from nf-core tools with nf-test.
  • [#32] - Update Stats workflow with nf-core modules for merging.
  • [#81] - Update Eval workflow with nf-core modules for merging.
  • [#111] - Fix linting warnings (mostly versions).
  • [#134] - Code revision for release preparation.
  • [#138] - MultiQC as nf-core module and fix visualization.
  • [#152] - Ignore kalign error 132 and print a warning (incompatibility with some CPU types).
  • [#153] - Fix time parser in shiny app.
  • [#154] - Fix metromap.
  • [#155] - Fix typos.

Dependencies

Deprecated