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poseidon-framework/poseidon-eager: Changelog

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

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.

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

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

v0.2.0dev - 25/04/2023

Added

  • scripts/source_me.sh: Includes various helper functions for all other scripts.
  • scripts/create_eager_input.sh: Script to create a preliminary nf-core/eager input TSV from a SSF file.
  • scripts/download_ena_data.py: Python script to read SSF file, download FastQs from the ENA, and create a file of expected md5sums.
  • scripts/run_download.sh: Wrapper script to submit the FastQ download job to the local MPI-EVA cluster.
  • scripts/validate_downloaded_data.sh: Script to validate the downloaded data, and create the intended symlinks for running nf-core/eager.
  • Added a Changelog: CHANGELOG.md
  • scripts/run_eager.sh: Script to run nf-core/eager for all packages that need (re-)running.
  • scripts/submit_as_array.sh: Helper script for submitting eager jobs as an SGE array on the MPI_EVA cluster.
  • Github Issue templates
  • Github pull request template
  • @delphis-bot makes the template tsv_patch for a package executable.
  • @delphis-bot now only triggered on new PR comment, not edits.
  • Propagate versions of all config files used in nf-core/eager runs to config_profile_description.
  • scripts/download_and_localise_package_files.sh is a wrapper script that does all the steps of getting a package backbone ready for eagering. Quality of life script for testing, but will be superceded soon.
  • Added scripts/ssf_validator.py.

Fixed

Dependencies

Deprecated