nf-core/airrflow: Tarantallegra

Added #413 Bump versions to dev. #413 Updated nf-core template to v3.3.2. #413 Speeding up tests with smaller test data. #416 Update Takara protocol names and docs. Add Takara SMART-seq protocol. #416 Add first nf-test. #422 Template update to nf-core v3.4.1 #425 Add all nf-tests. #431 Update nf-test snapshots and acknowledgements. #436 Update amulety modules and version. #437 Bump versions to 4.4.0. #441 Bump versions to 5.0, small syntax and docs fixes. Fixed #413 Add amulety versions in multiQC report. #413 Fixed bug in sans-umi worklfow revpr parameter. #416 Subsample reads for report_threshold process. #416 Removed a variable that was defined twice. #416 Renamed define_clones to clonal_assignment. #416 Fixed bug in number of sequences report. #416 Fixed bug in report file size. #422 Fixed annoying automatic clonal threshold message on any failure. #418 Fixed reassign false option and added tests. Dependencies | Dependency | Old version | New version | | ---------- | ----------- | ----------- | | enchantr | 0.1.20 | 0.1.24 | | presto | 0.7.4 | 0.7.6 | | dowser | 2.3 | 2.4.0 | | amulety | 1.0 | 2.1.1 | | multiqc | 1.27 | 1.32 | | trust4 | 1.0.13 | 1.1.5 | Deprecations and changes The clontech_umi_tcr protocol has been renamed to takara_smartseq_umi_tcr to reflect the new protocol name.