1.0.0

v1.0.0 - 02/09/2025

Added

• Minotaur.config -> 1.0.4:
  • New custom_minotaur_config_version and custom_minotaur_config_base params, to allow integration with the minotaur-institutional-configs repository.
• run_eager.sh:
  • Added -p/--profile option to specify the Nextflow profiles to use for Minotaur runs. This allows for more flexibility in running Minotaur with different configurations.
• validate_downloaded_data.sh: Fix validation of downloaded bam files.

Fixed

Dependencies

Deprecated

• Removed conf/EVA_cluster.config. Cluster configurations are now in the minotaur-institutional-configs repository.

0.5.1

v0.5.1 - 06/08/2025

Added

• populate_janno.py:
  • Adjusted to use sample_accession when secondary_sample_accession is not "n/a". This is important for data pulled from the GSA.

Fixed

• download_ena_data.py:
  • Fixed a bug where the md5sums of downloaded BAMs were formatted incorrectly in the expected_md5sum file.

Dependencies

Deprecated

• Removed packages/ directory, which included an early version of what has become the minotaur-recipes repository.

0.5.0

v0.5.0 - 06/05/2025 (mapdamage added on 05/11/2024)

Added

• minotaur_packager.sh:
  • Can now pick up mapdamage results when generating minotaur packages.
• download_ena_data.py now downloads BAMs in submitted_ftp when fastq_ftp is empty.
• conf/minotaur.config updated to run input BAM conversion back to FastQ for re-mapping.
• populate_janno.py:
  • Added mapdamage2 to the list of allowed damage calculation tools.
  • nf-core/eager version is now inferred from the pipeline information, and no longer hard-coded.

Fixed

Dependencies

• pyeager==0.1.5.0

Deprecated

0.4.0dev

v0.4.0dev - 08/10/2024

Added

• Updated Minotaur.config to include an adapter list. This ensures PE ssDNA data is processed correctly.
• Use mapdamage2 for damage calculation in eager. Now limiting damage calculation to 1M reads, instead of all.
• minotaur_packager.sh:
  • Minotaur packages are now sorted by ascending Poseidon_ID, to ensure stability across any reruns.
  • All Minotaur packages contain Thiseas C. Lamnidis as a contributor (i.e. to whom users should direct questions regarding processing etc).
  • Now includes -i/--interactive option to help debug janno fill-in errors.
• run_eager.sh: Now using nf-core/eager 2.5.1.

Fixed

• populate_janno.py: Small bugfix to remove duplicate sample names when multiple libraries of a sample exist.
• source_me.sh:
  • Removed some obsolete functions
  • symlink_names_from_ena_fastq() Can now deal with merged PE data, which produce 3 FastQs. Only merged reads will be kept for processing.

Dependencies

• nf-core/eager=2.5.1
• poseidon-trident=1.5.4.0
• pyeager=0.1.4.3
• argparse=1.4.0

Deprecated

• Removed some more scripts that have moved to the minotaur-recipes repo.

0.3.0dev

v0.3.0dev - 03/04/2024

Added

• Removed various scripts that have moved to the minotaur-recipes repo.
• scripts/download_ena_data.py can now download PE data
• scripts/minotaur_packager.sh:
  • Add option to force package recreation (but not publishing)
  • Add SSF to packages, and versions in README instead of txt file.
• scripts/populate_janno.py:
  • Add endogenous, captureType, udg, library_built, accessions, pipeline URL, and Genotype ploidy.
• scripts/run_eager.sh & scripts/download_and_localise_package_files.sh: Swap to variable for local paths to minotaur resources (more portable).
• Deactivated GA for validation that now moved to other repo.
• Updated PR template
• Configs now use tagged release for referencing cofs/assets

Fixed

Dependencies

Deprecated

0.2.1 - 2023-11-02

v0.2.1dev - 02/11/2023

Added

• scripts/minotaur_packager.sh: Script to create poseidon half-packages and fill in janno from eager results
• scripts/populate_janno.py: Script to fill in janno files with poseidon metadata from nf-core eager results.

Fixed

• scripts/validate_downloaded_data.sh: Add helptext
• scripts/run_eager.sh: Now uses big_data profile
• Updates to templates for packages and configs. These are now defunct as they are pulled from the minotaur-recipes repo, and will be removed in netx release.
• scripts/download_and_localise_package_files.sh distinction between symlink dir and package_eager_dir.

Dependencies

• nf-core/eager=2.4.6

Deprecated

0.2.0 - 2023-08-14

Initial release of Minotaur. Still in dev, but used for some packages, so requires a stable release.