Main changes are conversion from nextflow DSL1 to DSL2. Additionally, the template and software was updated, as detailed below. Changed #56 - Switched to DSL2 & update to new nf-core 2.1 TEMPLATE #56 - --krakendb now expects a .tar.gz/.tgz (compressed tar archive) directly from https://benlangmead.github.io/aws-indexes/k2 instead of an uncompressed folder. Added #56 - Added full size test dataset, two Zetaproteobacteria sequenced with Illumina MiSeq Reagent Kit V2, PE250, 3 to 4 million read pairs. Fixed #51 - Fixed Unicycler Dependencies #56 - Updated a bunch of dependencies (unchanged: FastQC, Miniasm, Prokka, Porechop, QUAST) Unicycler from 0.4.4 to 0.4.8 Kraken2 from 2.0.9beta to 2.1.1 MultiQC from 1.9 to 1.10.1 PYCOQC from 2.5.0...
[2.3] - 2022-02-04 :warning: Major enhancements Please see Major updates in v2.3 for a more detaile...
Template Fixed an issue regarding explicit disabling of unused container engines [#972] Removed tra...
[3.7] - 2022-05-03 :warning: Major enhancements Updated default STAR version to latest available (2...
This is basically a maintenance update that includes template updates, fixed environments and some m...
Added #73 - Add support for the non-free NetMHC tool family #83 - Add option for threshold custo...
v2.0 - Palladium Platypus - [2021-07-13] :warning: Major enhancements & breaking changes This marks ...
[2.0] - 2022-11-30 :warning: Major enhancements Samplesheet format has changed from group,replicate...
Another big release that's been coming for quite some time (apologies to all who have been running w...
Added #687 - Adds Kraken2 unique kmer counting report #676 - Refactor help message / summary messag...
When we do releases, we sometimes like to go big. This is one of those times. This is a truly huge r...
nf-core/ampliseq version 2.1.0 "Gray Steel Boa" - 2021-09-14 Summary of changes Updated documentati...
⚠️ Please read This release goes together with a major update on nf-core/modules that restructures D...
Initial release of nf-core/rnaseq! This release marks the point where the pipeline was moved from S...
[1.5] - 2021-12-01 Finish porting the pipeline to the updated Nextflow DSL2 syntax adopted on nf-co...
Initial release of nf-core/bacass, created with the nf-core template. This pipeline is for bacterial...
[2.3] - 2022-02-04 :warning: Major enhancements Please see Major updates in v2.3 for a more detaile...
Template Fixed an issue regarding explicit disabling of unused container engines [#972] Removed tra...
[3.7] - 2022-05-03 :warning: Major enhancements Updated default STAR version to latest available (2...
This is basically a maintenance update that includes template updates, fixed environments and some m...
Added #73 - Add support for the non-free NetMHC tool family #83 - Add option for threshold custo...
v2.0 - Palladium Platypus - [2021-07-13] :warning: Major enhancements & breaking changes This marks ...
[2.0] - 2022-11-30 :warning: Major enhancements Samplesheet format has changed from group,replicate...
Another big release that's been coming for quite some time (apologies to all who have been running w...
Added #687 - Adds Kraken2 unique kmer counting report #676 - Refactor help message / summary messag...
When we do releases, we sometimes like to go big. This is one of those times. This is a truly huge r...
nf-core/ampliseq version 2.1.0 "Gray Steel Boa" - 2021-09-14 Summary of changes Updated documentati...
⚠️ Please read This release goes together with a major update on nf-core/modules that restructures D...
Initial release of nf-core/rnaseq! This release marks the point where the pipeline was moved from S...
[1.5] - 2021-12-01 Finish porting the pipeline to the updated Nextflow DSL2 syntax adopted on nf-co...
Initial release of nf-core/bacass, created with the nf-core template. This pipeline is for bacterial...
[2.3] - 2022-02-04 :warning: Major enhancements Please see Major updates in v2.3 for a more detaile...
Template Fixed an issue regarding explicit disabling of unused container engines [#972] Removed tra...
[3.7] - 2022-05-03 :warning: Major enhancements Updated default STAR version to latest available (2...