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

[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

Deprecated

• Deprecated param enable_conda

Contributors

@ssnn-airr and @ggabernet

[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

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

Deprecated

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

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

| 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.

⚠️ Major enhancements

• The pipeline has been ported to Nextflow DSL2
• Analysis of TCR repertoires is now also supported
• Added Rmarkdown report with a summary of the repertoire analysis
• Analysis of data with RACE 5’ protocol is now supported
• Scripts to download and build new versions of the IMGT database have been added
• Improvement of UMI handling and possibility to exchange position of C and V-primers
• Updated to new versions of Immcantation Framework, providing support for the AIRR format

Please check the CHANGELOG for more details.

Released on 14 January 2020. Check the Changelog for more information.

Added

• Handle barcodes that are already merged to R1 or R2 reads
• Validate inputs and cluster threshold
• --downstream_only feature
• Handle of UMIs of different lengths
• --skipDownstream feature
• Add github actions ci testing

Fixed

• #51 - Fixed MaskPrimers bug
• #45 - Fixed UMI reading from R1 or R2 & UMI length
• #57 - Improved results directory organization
• #55 - Dropped Singularity file

Version 1.1.0 adds functionality to the pipeline. The main added features of this release are the calculation of the B-cell clones in a patient-wide way and the downstream repertoire analysis.

Added

• Merging all the repertoires from the same patient
• Added clone calculation per patient: --set_cluster_thresholdand cluster_threshold parameters.
• Added downstream analysis processes: diversity, abundance, mutational load, Ig type and gene distribution
• Parsing logs for all processes
• FastQC and multiQC processes
• Option for providing Illumina index and UMI as part of R1
• Update template to tools 1.7

Fixed

• #25 - Improved documentation
• #27 - Added FastQC and MultiQC processes
• #21 - Added log parsing

Dependencies

• Update Nextflow 0.32.0 -> 19.10.0
• Added several requirements for downstream analysis.

Deprecated

v1.0.0 - 2019-04-16 - “Alohomora”

Initial release of nf-core/bcellmagic, created with the nf-core template.