v 1.1.0 - 2024-02-10 - Tremendous Wombat

v1.1.0 - [2024-02-10]

Credits

Special thanks to the following for their input and contributions to the release:

• Jens Luebeck
• Simon Pearce
• Maxime U Garcia
• Alex M. Ascensión

Enhancements & fixes

• Nf-core template update to 2.11.1
  • update of nf-core modules versions
• Removed AmpliconArchitect and AmpliconClassifier modules with their respective scripts in /bin
  • AmpliconArchitect and AmpliconClassifier is now run inside the AmpliconSuite-Pipeline. Additional scripts are not necessary.
  • Removed respective configs and workflow code
• Added AmpliconSuite-Pipeline
  • A wrapper for calling copy numbers, preparing amplified intervals, running AmpliconArchitect, and calling amplicon classes using AmpliconClassifier
  • Added docker container named PrepareAA to run AmpliconSuite-Pipeline with singualarity or docker
  • Added module configs and description
• Changed assets/multiqc_config.ymlto fit new pipeline version
• Included directory checks for mosek_license_dir and aa_data_repo .
  • Removed both directory parameters in the test profile as it is only checked when running ampliconarchitect
• Updated nextflow_schema.json to give better details about how to use --circle_identifier
• made --circle_identifier an essential parameter
• made --input_format an essential parameter and removed the default value to request specification by user
• Updated --bwa_index to accept only directory paths to the bwa index files. Makes the user input easier to not need to deal with file endings and patterns. Bug identified by Alex M. Ascensión in #68