airrflow - v4.3.1 Revelio bugfix

Added

• #399 Bump versions.

Fixed

• #392 Updated tutorials.

- Nextflow
Published by ggabernet about 1 year ago

airrflow - 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 |

- Nextflow
Published by ggabernet about 1 year ago

airrflow - 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 isotypecolumn parameter in favor of annotating C region from internal cregion alignment or cprimer alignment into the ccall 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.

- Nextflow
Published by ggabernet over 1 year ago

airrflow - 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 |

- Nextflow
Published by ggabernet about 2 years ago

airrflow - [4.0] - 2024-04-23 Ascendio

Added

• #319 Added AIRR compliance badge

Fixed

• #319 Fix test full profile and nebnextumitcr 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.

- Nextflow
Published by ggabernet over 2 years ago

airrflow - 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 |

- Nextflow
Published by ggabernet over 2 years ago

airrflow - 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

- Nextflow
Published by ggabernet over 2 years ago

airrflow - [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 |

- Nextflow
Published by ggabernet about 3 years ago

airrflow - 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

- Nextflow
Published by ggabernet over 3 years ago

airrflow - 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

- Nextflow
Published by ggabernet over 3 years ago

airrflow - 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

- Nextflow
Published by ggabernet almost 4 years ago

airrflow - 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

- Nextflow
Published by ggabernet about 4 years ago

airrflow - 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.

- Nextflow
Published by ggabernet about 4 years ago

airrflow - nf-core/bcellmagic version 2.0.0 "Lumos"

:warning: 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.

- Nextflow
Published by ggabernet about 5 years ago

airrflow - 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

- Nextflow
Published by ggabernet over 6 years ago

airrflow - 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

- Nextflow
Published by ggabernet over 6 years ago

airrflow - 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.

- Nextflow
Published by ggabernet over 7 years ago