Added

• #407 Added genotyping sub-workflow.
• #424 Added support for AIRR-C germline reference.

Fixed

• #420 Fixed a bug in the Alakazam collapseDuplicates function.
• #411 Fixed a bug in Enchantr dowser_lineage project.
• #453 Fix publishDir collisions in PRESTO_PARSE_CLUSTER and PRESTO_PAIRSEQ_CLUSTERSETS.
• #469 Fixed bug with param --skip_report.

Dependencies

Deprecations and changes

• #451 Removed repertoire analysis from clonal assignment report. Added repertoire report which includes clone size distribution, clonal abundance, diversity, clonal overlap and mutation frequency.
• The param fetch_imgt has been updated to fetch_germlines and it now accepts the options none, imgt or airrc-imgt.
• The param save_databases has been updated to save_germlines.

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

Deprecations and changes

• The clontech_umi_tcr protocol has been renamed to takara_smartseq_umi_tcr to reflect the new protocol name.

Added

• #399 Bump versions.

Fixed

• #392 Updated tutorials.

Added

• #360 Update pipeline diagrams.
• #374 Template update to nf-core v3.2.0.
• #373 Added bulk and single-cell tutorials.
• #377 Added Amulety translation and embeddings.
• #379 Added embeddings to full size tests.
• #379 Added option to skip clonal analysis.
• #384 Bumped versions to 4.3.0.

Fixed

• #378 Updated primer links to Immcantation GitHub.
• #384 Temporarily downgrade nf-schema to fix compatibility with NXF > 25.03.1-edge

Dependencies

Added

• #334 Added TRUST4 support.
• #344 Added option to remove V and C primer region when sequence is unknown.
• #344 Added option to save non-productive sequences
• #344 Allow for maskprimers align with UMI on both V gene and C gene primers.
• #344 Update pipeline template to nf-core tools v3.0.2.
• 357 Deprecate isotype_column parameter in favor of annotating C region from internal c_region alignment or c_primer alignment into the c_call column.

Fixed

• #344 Avoid saving pRESTO intermediate fastq files in results directory.
• #344 Simplified pRESTO Maskprimers score and Maskprimers extract processes.
• #344 Fix clustersets approach, consider both reads clusters annotation.
• #344 Allow for partial alignments in MakeDB for mouse TCR data, to bypass junction check for TRAV germlines with additional positions (e.g. 84A).
• #344 Fix parse logs merging dataframes using pandas join to produce logs even when there are failing samples.
• #344 Use pRESTO Collapseseq with n=0 by default due to runtime issues.

Dependencies

Deprecated parameters

• isotype_column: if c_call column value is NA, now c_region and c_primer column values respectively are annotated into the c_call column.

Added

• #335 Update to nf-core template 2.14.1

Fixed

• #335 Fix report number of sequences per sample plots.

Dependencies

Added

• #319 Added AIRR compliance badge

Fixed

• #319 Fix test full profile and nebnext_umi_tcr profile.
• #321 Label Dowser tips by isotype instead of c_call by default.
• #322 Use RAxML as the default builder for dowser. Skip lineage trees by default.

Dependencies

Deprecated parameters

• --skip_lineage_trees is now deprecated in favor of --lineage_trees. Lineage trees are skipped by default.
• --igphyml parameter is deprecated in favor of --lineage_tree_exec. All lineage tree building software part of Dowser are now supported.
• --igblast_base is deprecated in favor of --reference_igblast.
• --imgtdb_base is depracated in favor of --reference_fasta.

Added

• #294 Merge template updates nf-core/tools v2.11.1
• #299 Add profile for common NEB and TAKARA protocols
• #289 Add possibility to merge multi-lane samples when starting from fastq files
• #289 Add possibility to run cellranger for scVDJseq data

Fixed

• #294 Removed optional output from FilterQuality to not fail silently
• #293 Clonal_threshold is validated to be 'auto' or number greater than zero
• #295 Fixed airrflow report sequence plot and add path to clonal analysis reports
• #310 Bump versions to 3.3.0, update containers and software versions

Dependencies

[3.2.0] - 2023-10-27 Expecto patronum

Added

• #268 Added parameters for FindThreshold in modules.config.
• #268 Validate samplesheet also for assembled samplesheet.
• #259 Update to EnchantR v0.1.3.
• #266 Added clonal reports tables to final report folder.
• #266 Added processes to include sampleID to filename in assembled workflow to keep it unique.
• #276 Parametrize FindThreshold Report and Presto Buildconsensus UMI.
• #281 Update to nf-core tools v2.10.

Fixed

• #268 Allows for uppercase and lowercase locus in samplesheet pcr_target_locus.
• #259 Samplesheet only allows data from one species.
• #259 Introduced fix for a too long command with hundreds of datasets.
• #266 Convert samplesheet required columns to strings when needed.
• #284: Use cached IMGT and IgBlast reference data by default.

Dependencies

Contributors: @ssnn-airr @ggabernet @mdeboth

Added

• #250 Back to dev.
• #256 Merge template updates to nf-core tools 2.8.
• #263 Bump versions to 3.1.

Fixed

• #250 Fixed log parsing with removeprefix instead of lstrip.
• #258 Fixes to plotly plots in report sometimes not rendering.
• #258 Remove direct call to Igblast in favor of a fix in ChangeO.
• #258 Added check for whitespaces in certain columns in samplesheet.
• #258 Added missing Immcantation references in Airrflow report.

Dependencies