Releases: nf-core/airrflow
Releases · nf-core/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 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
| 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.
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
