Recent Releases of targene-pipeline
targene-pipeline - v0.11.1
What's Changed
- Bugfix by @roskamsh in https://github.com/TARGENE/targene-pipeline/pull/206
- Test if continuous integration is faulty by @roskamsh in https://github.com/TARGENE/targene-pipeline/pull/208
- Allofus - Adapt targene for use on the All of Us Researcher Workbench by @roskamsh in https://github.com/TARGENE/targene-pipeline/pull/174
- Create Estimators files if "string mode" is specified for ESTIMATORS_CONFIG parameter in https://github.com/TARGENE/targene-pipeline/pull/210
Reviewed by @olivierlabayle
Full Changelog: https://github.com/TARGENE/targene-pipeline/compare/v0.11.0...v0.11.1
- Nextflow
Published by roskamsh over 1 year ago
targene-pipeline - v0.11.0
Post Thesis release.
New features.
- GWAS (@joshua-slaughter, @roskamsh, @olivierlabayle)
- REALISTICSIMULATION, NULLSIMULATION workflows for the evaluation of PopGen semi-parametric estimators (@olivierlabayle).
- ESTIMATORS_CONFIG via either a file or a modular configuration string (@olivierlabayle).
- Improved documentation and examples (@olivierlabayle)
Deleted.
- STUDYDESIGN parameter, all study designs are part of the ESTIMANDSCONFIG parameter
- FROM_ACTORS study design
Reviewed by @roskamsh.
Full Changelog: https://github.com/TARGENE/targene-pipeline/compare/v0.10.0...v0.11.0
- Nextflow
Published by olivierlabayle almost 2 years ago
targene-pipeline - v0.10.0
- Add flat config [BREAKING]
- start to rework docs
- Nextflow
Published by olivierlabayle over 2 years ago
targene-pipeline - v0.9.1
Fix potential concurrency issue in longest_prefix function
- Nextflow
Published by olivierlabayle over 2 years ago
targene-pipeline - v0.9.0
Breaking Release.
New Features:
- CV-TMLE / CV-OSE
- Arbitrary number of estimators
- Composed Estimands in particular allele independent interactions with STUDYDESIGN="ALLELEINDEPENDENT"
- SNP or Trait specific models can be provided on top of the default config
What's Changed
- Refactor by @olivierlabayle in https://github.com/TARGENE/targene-pipeline/pull/119
- Argparse by @olivierlabayle in https://github.com/TARGENE/targene-pipeline/pull/133
Full Changelog: https://github.com/TARGENE/targene-pipeline/compare/v0.8.0...v0.9.0
- Nextflow
Published by olivierlabayle over 2 years ago
targene-pipeline - v0.8.0
- Add Support for custom Datasets: @roskamsh
- Add Support for multi TF runs: @roskamsh
- Nextflow
Published by olivierlabayle over 2 years ago
targene-pipeline - v0.7.2
- Hopefully fix LD thining memory issue
- Nextflow
Published by olivierlabayle over 2 years ago
targene-pipeline - v0.7.1
Fix compat sieve variance
- Nextflow
Published by olivierlabayle almost 3 years ago
targene-pipeline - v0.7.0
- Remove genotypeasint
- Move to Arrow tmle_input dataset
- Nextflow
Published by olivierlabayle almost 3 years ago
targene-pipeline - v0.6.2
- Documentation update
- Nextflow
Published by olivierlabayle almost 3 years ago
targene-pipeline - v0.6.1
Add weighted fluctuation
- Nextflow
Published by olivierlabayle almost 3 years ago
targene-pipeline - v0.6.0
Adds:
- New estimator file format
- Control over cross validation for GLMNet
- Nextflow
Published by olivierlabayle about 3 years ago
targene-pipeline - v0.5.0
Breaking: Yes
New:
- New parameter file format (breaking)
- Automatic p-value adjustment by trait
- Negative control pipeline
- Nextflow
Published by olivierlabayle about 3 years ago
targene-pipeline - v0.4.0
New features:
FROM_ACTORSmode:
- Will now also compute the Average treatment effect with fixed treatments other than the bQTL. This will hopefully provide the directionality of effect to the current interaction results!
- Can support both string ("AA", "AC", "CC") and integer (0,1,2) representation of alleles vias the
GENOTYPES_AS_INTargument (default to false)
- We now have working tests and CI at the pipeline level!
- All internal releases now follow semantic versioning!
- The new
SAVE_ICargument (default to true) allows to save influence curves with p-value under 'SIEVEPVAL' independently of whether you want to compute the sieve estimates (`NBVAR_ESTIMATORS` > 0).
- Nextflow
Published by olivierlabayle about 3 years ago
targene-pipeline - v0.3.2
fix typo for extra covariates
- Nextflow
Published by olivierlabayle over 3 years ago
targene-pipeline - v0.1.1
Changes:
- Incorporate new TMLE image from new TargetedEstimation repo
- Fix bug: NbPhenotypes in groupTuple clause
- Nextflow
Published by olivierlabayle almost 4 years ago