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

nf-core/airrflow version 3.2.0 "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

nf-core/airrflow version 2.4.0 "Aparecium"

[2.4.0] 2022-12-05 "Aparecium"

Minor release adding fastp.

Added

• #209 Template update to nf-core tools v2.6.
• #210 Add fastp for read QC, adapter trimming and read clipping.
• #212 Bump versions to 2.4.0

nf-core/airrflow version 2.3.0 "Expelliarmus"

Added

• #180 Added possibility to add any property in the AIRR sequence table as label on the lineage tree nodes.
• #180 Lineage tree construction now also includes trees with just one sequence.
• #180 Added metadata annotation to final repertoire table.
• #180 Added possibility to provide custom Rmarkdown report.
• #183 Update template to nf-core tools v2.5.1
• #183 Add option to provide another different threshold in splitseq process

Fixed

• #180 Repertoire analysis report now also saves diversity table.

Dependencies

Dependency	Old version	New version
multiqc	1.12	1.13

Deprecated

nf-core/airrflow version 2.2.0 "Reparo"

Added

• Pulling IMGT database cache from aws for CI tests.
• Added test to pull database from IMGT and build it with igblast.
• Template update to nf-core tools v2.4.1.
• Added zipped DB cache to nf-core/test-datasets.

Fixed

• Updated container of Fetch databases and Changeo_assigngenes process to Changeo=1.2.0 and Igblast=1.17.1and extended biocontainers base to have internet access.
• Fixed publishing directory mode for all modules.

Dependencies

Deprecated

nf-core/airrflow version 2.1.0 "Accio"

Main new features

• Added possibility of processing BCR / TCR amplicon data without UMI barcodes.
• Sample sheet now follows the AIRR standard.
• Added option to skip clustering sequences according to similarity (pRESTO ClusterSets).

Added

• #130: Organized presto processes in presto_umi subworkflow.
• #128: Added presto_sans_umi subworkflow option. Added postassembly FastQC and corresponding section in MultiQC. Included refs for analysis of light chains (if present) by default.
• updated docs for --library_generation_method parameter.
• Samplesheet column names were updated to follow the AIRR standard.
• Fixed docs on --umi_start parameter, this parameter should only be used when UMIs are provided in the index reads.
• #143 Template update to nf-core tools v2.2.
• #150 Added option to search for reverse primers.
• #159 Template update to nf-core tools v2.3.1, v2.3.1
• #161 Add option to skip clustering sequences in the UMI workflow
• #163 Added process labels and software version emitting to all modules. Fixed output folder name for changeo processes.
• Bump versions to 2.1.0

Fixed

• #150: Fixed cprimer start position, when cprimer in R2 reads.
• Remove need for a plot when Hamming threshold cannot be generated.
• The shazam threshold process is not executed when the hamming threshold is provided.
• #164: Fixed AWS tests when running on fusion mounts, solving #137.

Dependencies

Dependency	Old version	New version

| igblast | 1.15.0 | 1.17.1 |
| presto | 0.6.2 | 0.7.0 |
| changeo | 1.0.2 | 1.2.0 |
| r-base | 4.0.3 | 4.1.2 |
| r-alakazam | 1.0.2 | 1.2.0 |
| r-shazam | 0.1.11 | 1.1.0 |
| r-tigger | 0.3.1 | 1.0.0 |

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if new version information isn't present.

Deprecated

• Parameter --protocol was updated to --library_generation_method to follow the AIRR standard.
• Parameter --loci and --species were converted to a column in the samplesheet (pcr_target_locus and species) to allow processing simultaneously TR and IG loci from the same sample, also allow processing different species in one samplesheet.
• Removed genotyping step with tiGGer.