Releases: poseidon-framework/poseidon-eager
Releases · poseidon-framework/poseidon-eager
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 datascripts/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 resultsscripts/populate_janno.py
: Script to fill in janno files with poseidon metadata from nf-core eager results.
Fixed
scripts/validate_downloaded_data.sh
: Add helptextscripts/run_eager.sh
: Now usesbig_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.