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.

nf-core/bcellmagic version 2.0.0 "Lumos"

⚠️ 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.

nf-core/bcellmagic version 1.2.0 "Riddikulus"

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

nf-core/bcellmagic version 1.1.0 "Wingardium Leviosa"

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

nf-core/bcellmagic version 1.0.0 "Alohomora"

v1.0.0 - 2019-04-16 - "Alohomora"

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