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.

v4.3.1 Revelio bugfix

Added

• #399 Bump versions.

Fixed

• #392 Updated tutorials.

v4.3.0 - Revelio

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

Dependency	Old version	New version
enchantr	0.1.16	0.1.20
presto	0.7.1	0.7.4
dowser	2.1	2.3
alakazam	1.3.0	1.3.1

v4.2.0 Evanesco

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

Dependency	Old version	New version
enchantr	0.1.16	0.1.19
presto	0.7.1	0.7.2

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.

v4.1.0 Avenseguim

Added

• #335 Update to nf-core template 2.14.1

Fixed

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

Dependencies

Dependency	Old version	New version
biopython	1.71	1.81
enchantr	0.1.15	0.1.16
scoper	1.2.1	1.3.0
dowser	1.2.0	2.1.0
igphyml	1.1.5	2.0.0

[4.0] - 2024-04-23 Ascendio

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

Dependency	Old version	New version
enchantr	0.1.11	0.1.14

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.

3.3.0 - 2024-03-31 Confringo

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

Dependency	Old version	New version
multiqc	1.19	1.21
enchantr	0.1.9	0.1.11
igblast	1.19.0	1.22.0

v3.2.0 "Expecto patronum"

[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

Dependency	Old version	New version
r-enchantr	0.1.2	0.1.9
r-alakazam	1.2.1	1.3.0
r-shazam	1.1.0	1.2.0
r-dowser	1.2.0	2.0.0
fastqc	0.11.9	0.12.1

Contributors: @ssnn-airr @ggabernet @mdeboth

[3.1.0] - 2023-06-05 "Protego"

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

Dependency	Old version	New version
r-enchantr	0.1.1	0.1.2
multiqc	1.13	1.14
fastp	0.23.2	0.23.4

nf-core/airrflow version 3.0 "Portus"

[3.0] - 2023-03-20 "Portus"

Added

• #197 Combined old bcellmagic and reveal subworkflows for better pipeline integration.
• #197 Added compulsory AIRR fields in input samplesheet.
• #197 Added option to calculate clones per group clone_by and then create a report with the results altogether.
• #197 Added pipeline overview diagram and metro map.
• #197 Added full logs to enchantr report filesize process.
• #215 Template update to nf-core tools v2.7.1.
• #224 Template update to nf-core tools v2.7.2.
• #225 Added plotly interactive reports.
• #225 Added find threshold report even when specifying clonal threshold.
• #225 Added possibility to provide direct call to igblast.
• #228 Improved docs preparing release.
• #244 Bump versions to 3.0.

Fixed

• #221 Fixed bug arising when not providing --index_file FALSE for some input options not requiring index files.
• #239 Implemented workaround for Slurm Sbatch file too large. We plan to revert when possible#242
• #245 Add missing module versions
• #248 Applied review comments by @adamrtalbot @louperelo, thank you!
• #249 Do not run tests with immcantation container when doing a PR to master.

Dependencies

Dependency	Old version	New version
multiqc	1.13	1.14
pandas	1.1.5	1.5.3
presto	0.7.0	0.7.1
changeo	1.2.0	1.3.0
igblast	1.17.1	1.19.0
r-enchantr		0.1.1
r-plotly		4.10.1

Deprecated

• Deprecated param enable_conda

Contributors

@ssnn-airr and @ggabernet