1.6.3

v1.6.3
27/10/2025
  DOCUMENTATION
  * Better help message for the pipelines (Issue #112)
  BUGFIXES
  * Resolve the bug where the checker adds dependencies to the search stage and inference step : AlphaFold2, AlphaFold3, afMassive, ColabFold (Issue #105)
  * Resolve creation of the AlphaBridge folder :  AlphaFold2, afMassive, ColabFold (Issue #106)
  * Resolve the help bug when --outDir is selected (Issue #109) 
  * Remove printing on DiffDock, DynamicBind (Issue #111)
  - NanoBert:
    * Resolve the bug in the creation of Singularity container (Issue #110)

v1.6.2

v1.6.2
18/07/2025
BUGFIXES

AlphaFold3:

Resolve bug when option --num_seeds : erreur to addresse the content of alphafold3Options to bash variable (Issue #102)

v1.6.1

v1.6.1
06/06/2025
BUGFIXES

• AlphaBrige:
  • add the files generated by Alphabridge in bin/ap_generate_yaml_4_plots.sh to display graphs in MultiQC (Issue #100)
• python-env:
  • defaults -> nodefaults

v1.6.0

v1.6.0
05/20/2025

NEW FEATURES

• AlphaFold3:
  • Add AlphaBridge in multiqc report (Issue #92)
  • Seed parallelization (Issue #90)
• AfMassive:
  • Added a default value of false for launchAfMassive (Issue #88)
• Error added if option --random_seed not provided for AlphaFold2, afMassive, ColabFold (Issue #87)

BUGFIXES

• Test added for onlyMsas (Issue #89)
• Added command test in Admin.md (Issue #89)
• Resolve error for onlyMsas (Issue #89)
• Added Json or Fasta Checker result to foldSearch processes to respect script order (Issue #79)
• DiffDock:
  • no longer recalculates .npy files on each run (Issue #95)
• AlphaFold3:
  • Resolve bug when len modelSeeds = 1 and numSeeds is None (Issue #98)

DOCUMENTATION
- git setting for HuggingFace (NanoBert) (Issue #93)

v1.5.0

v1.5.0
01/24/2025

NEW FEATURES

• AlphaFold3 updated with v3.0.1

v1.4.0

v1.4.0
01/13/2025

NEW FEATURES

• AlphaFold3
• Bootstrap using Docker containers on Docker Hub 4geniac

BUGFIXES

• Remove double-quotes for boolean parameter in json files
• Numpy forced to version 1.26.4 in nanoBERT container

DOCUMENTATION

• Detail outputs and explain how the different annotations must be installed
• Examples of different channels patterns explained in the nextflow code