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nf-core/airrflow: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[4.1.0] -

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] - 2024-04-22 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

[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

[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

[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

[2.4.0] 2022-12-05 "Aparecium"

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

[2.3.0] - 2022-09-22 "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
  • Rename reveal test to test_assembled, add separate test for immcantation devel container as another job so other tests are not cancelled if this test does not run through.

Fixed

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

Dependencies

Dependency Old version New version
multiqc 1.12 1.13

Deprecated

[2.2.0] - 2022-06-02 "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

[2.1.0] - 2022-05-02 "Accio"

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.

[2.0.0] - 2021-07-19 "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

Added

  • #69: Template update to nf-core tools v1.10.2
  • #69: Added parameter json schema
  • #74: Added possibility of setting UMI start position and better UMI docs
  • #85: Added primer handling params: --vprimer_start, --cprimer_start, --primer_mask_mode, --primer_maxeror, --primer_consensus
  • #85: Added support for TCR data with params: --loci
  • #85: Added support for mice data and possibility for other species with params: --species
  • #85: Added support for 5' RACE technology with params: --protocol, --race_linker
  • #87: Added tests for TCR data
  • #102: Added param --protocol.
  • #102: Added support for C-primer in any R1 or R2 with param --cprimer_position.
  • #102: Bump versions to 2.0.
  • #103: Added full size tests (pcr_umi).
  • #114: Added parameter --skip_lineages.
  • #112: Template update to nf-core tools v1.14.
  • #114: Added Bcellmagic html report.
  • #114: Improved documentation on amplicon protocol support.
  • #115: Improved output file structure and documentation.
  • #124: Template update to nf-core tools v2.0.1.

Fixed

  • #74: Fixed AWStest workflow
  • #75: Fixed lineage trees publish plots and graphml
  • #75: Assemble process shorten filename to avoid error due to too long filename
  • #87: Order sequence logs by sample ID.
  • #104: Fix bug in pairseq barcode copy before consensus.
  • #114: Analysis not restricted to Ig heavy chains.
  • #123: Fix report Rmarkdown reading for running on AWS.

Dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency Old version New version
Python v3.6.11 3.8.0,3.0.3
markdown v3.1.1
muscle v3.8.1551
vsearch v2.11.1
fastqc 0.11.8 0.11.9
multiqc 1.9 1.11
matplotlib 3.0.3
cd-hit 4.8.1
blast 2.7.1
igblast 1.10.0 1.15.0
phylip 3.697 3.697
airr 1.2.1
presto 0.5.10 0.6.2
changeo 0.4.5 1.0.2
biopython 1.70 1.74
pandas 0.24.2 1.1.5
seaborn 0.9.0
r-base 3.5.1 4.0.3
r-alakazam 0.2.11 1.0.2
r-shazam 0.1.11 1.0.2
r-tigger 0.3.1 1.0.0
r-dplyr 0.8.3 1.0.6
r-data.table 1.12.2
r-igraph 1.2.4.1
igphyml 1.1.3
wget 1.20.1

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 version information isn't present.

Deprecated

  • #69: --SkipDownstream param changed to --skip_downstream.
  • #69: --metadata param changed to --input
  • --saveDBs param change to --save_databases
  • Default for --umi_length changed to 0
  • #102: --race_5prime param deprecated in favor of --protocol.
  • --skip_downstream changed to --skip_report.

[1.2.0] - 2020-01-14 - "Riddikulus"

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

Dependencies

Deprecated

[1.1.0] - 2019-11-06 - "Wingardium Leviosa"

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

[1.0.0] - 2019-04-16 - "Alohomora"

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