nf-core/stableexpression v1.1.0 - Canis lupus

Added

• #58 Tries to fetch genome annotation from the Ensembl organisms FTP, in addition to Ensembl and NCBI.

Fixed

• #38 Fix bug with species having multiple entries in g:Profiler (like canis lupus). Now querying g:Profiler beforehand to get the exact list of available species
• #37 Fix too short time limit for IMPUTE_MISSING_VALUES module, which resulting in module failture for species comprising a large number of datasets, like homo sapiens, mus musculus, or arabidopsis thaliana
• #36 Check correspondance between Ensembl gene IDs obtained from g:Profiler and gene IDs contained in the downloaded genome annotation. Now multiple annotations are downloaded and the one displaying the greatest number of matching gene IDs is chosen. If no annotation displayed matching gene IDs, the module tries with NCBI genome annotation.
• #61 Fixed an issue with the R Bioconductor ExpressionAtlas package resulting in a bug when trying to download some experiments (for example Musa acuminata).

Changed

• #PR46 Updated to nf-core pipeline template v4.1.0
• #PR46 Changed default branch to main