nf-core/viralrecon 3.0.0 - Waterdog Hibiscus - 2025-10-28
Credits
Special thanks to the following for their code contributions to the release:
- Adam Talbot
- Joon Klaps
- Sarai Varona
- Jaime Ozáez
- Sara Monzon
- Matthias Hörtenhuber
- Anna Norén
- JC Jossart
- Leo Caparica
- Michael L Heuer
New Contributors
- @adamrtalbot made their first contribution in #387
- @Joon-Klaps made their first contribution in #375
- @CaparicaLeo made their first contribution in #483
- @jaimeozaez made their first contribution in #485
- @mashehu made their first contribution in #489
- @cjjossart made their first contribution in #509
- @AnnaNoren made their first contribution in #520
Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
What's Changed
Enhancements & fixes
- Bump pipeline version to 2.7.0dev by @drpatelh in #372
- Remove system exit 1 by @adamrtalbot in #387
- Adding new nf-core subworkflow freyja for weighted variant analysis by @Joon-Klaps in #375
- Important! Template update for nf-core/tools v2.9 by @nf-core-bot in #384
- Remove minia from default assembler by @adamrtalbot in #395
- Fixed conflicts and updated modulels for nf-core/tools version 2.11.1 by @svarona in #408
- Changed primer set to params by @svarona in #393
- Add parameter freyja_depthcutoff by @Joon-Klaps in #412
- Update multiqc & add freyja to MQC by @Joon-Klaps in #413
- Template update for nf-core/tools version 2.12 by @svarona in #416
- Template update for nf-core/tools v2.13.1 by @svarona in #424
- Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in #421
- Added option to add a custom annotation, clarified multiQC results and fixed issues by @svarona in #401
- 417 allow skipping freyja boot by @Joon-Klaps in #426
- Template update for nf-core/tools version 2.14.1 by @svarona in #430
- Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in #428
- Enhanced BLAST results filtering by @svarona in #434
- update fastp module by @Joon-Klaps in #438
- fix cardinality when params.bowtie2_index used by @Joon-Klaps in #439
- Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in #444
- Changed Cutadapt to use nf-core modules by @svarona in #435
- Update nextclade & pangolin modules by @Joon-Klaps in #446
- Patch nf schema - include integer & string as type for sample by @Joon-Klaps in #450
- Fix
ch_blast_dbto have correct cardinality for blast/blastn by @Joon-Klaps in #452 - Merging 3.1.0 and 3.1.1 template updates by @heuermh in #455
- Important! Template update for nf-core/tools v3.1.1 by @nf-core-bot in #454
- Template update for hackathon nf-core/tools v3.2.0 by @svarona in #464
- Important! Template update for nf-core/tools v3.2.0 by @nf-core-bot in #459
- Update ivar_variants_to_vcf.py: Bug Fixes, Merging Improvements & Refactor by @saramonzon in #469
- resolving redundancies by @CaparicaLeo in #483
- Update local modules versions by @svarona in #486
- Quick fix, test_full.config by @Joon-Klaps in #492
- Remove asciigenome by @svarona in #491
- Added kraken2 to nanopore workflow by @jaimeozaez in #485
- Update modules by @saramonzon in #494
- Switch CI to self hosted runners and update minimal nextflow version by @mashehu in #489
- Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in #496
- Template update for nf-core/tools v3.3.2. by @svarona in #505
- Important! Template update for nf-core/tools v3.3.2 by @nf-core-bot in #504
- Template update by @svarona in #506
- Use nf-core multiqc module and fixed missing reports by @svarona in #508
- Update multiqc implementation by @Joon-Klaps in #479
- Fix local component structure for #465 by @cjjossart in #509
- Fixed pipelines linting by @svarona in #511
- Some fixes prior to release by @svarona in #518
- Update metro map illumina, Issue #517 by @AnnaNoren in #520
- Template update for nf-core/tools v3.4.1 by @svarona in #533
- Important! Template update for nf-core/tools v3.4.1 by @nf-core-bot in #531
- Important fixes prior to release by @svarona in #523
- Pre-release changes by @svarona in #534
- Added environment.yml files to local modules and added full_aws_test by @svarona in #536
- Fixed freyja channels by @svarona in #537
- fixed software versions for conda by @svarona in #538
- Fix conda snaps by @svarona in #539
- Update artic version and fixed snaps by @svarona in #540
- fixed conda snaps by @svarona in #542
- Dev -> Master for 3.0 release by @svarona in #535
Parameters
| Old parameter | New parameter |
|---|---|
--skip_freyja |
|
--freyja_repeats |
|
--freyja_db_name |
|
--freyja_barcodes |
|
--freyja_lineages |
|
--skip_freyja_boot |
|
--additional_annotation |
|
--min_contig_length |
|
--min_perc_contig_aligned |
|
--skip_noninternal_primers |
|
--threeprime_adapters |
|
--freyja_depthcutoff |
|
--pango_database |
|
--nextclade_dataset_reference |
|
--skip_asciigenome |
|
--asciigenome_read_depth |
|
--asciigenome_window_size |
|
--fast5_dir |
|
--artic_minion_caller |
|
--artic_minion_aligner |
|
--artic_minion_medaka_model |
--artic_minion_model_dir |
NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.
Software 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 |
|---|---|---|
asciigenome |
1.16.0 | |
artic guppyplex |
1.2.3 | 1.6.2 |
artic minion |
1.2.3 | 1.6.2 |
bandage |
0.8.1 | 0.9.0 |
bcftools |
1.16 | 1.22 |
bedtools |
2.30.0 | 2.31.1 |
biopython |
1.79 | 1.85 |
biostrings |
2.58.0 | 2.66.0 |
blast |
2.13.0 | 2.16.0 |
bowtie2 |
2.4.4 | 2.5.4 |
complexheatmap |
2.6.2 | 2.14 |
coreutils |
9.4 | 9.5 |
cutadapt |
4.2 | 5.0 |
fastp |
0.23.2 | 1.0.1 |
fastqc |
0.11.9 | 0.12.1 |
freyja |
2.0.1 | |
grep |
3.4 | 3.11 |
gzip |
1.13 | |
htslib |
1.20 | 1.22.1 |
ivar |
1.4 | 1.4.4 |
kraken2 |
2.1.2 | 2.1.6 |
lbzip2 |
2.5 | |
matplotlib |
3.5.1 | 3.10.1 |
mosdepth |
0.3.3 | 0.3.11 |
multiqc |
1.14 | 1.31 |
nanoplot |
1.41.0 | 1.46.1 |
nf-schema |
2.2.1 | |
nextclade |
2.12.0 | 3.11.0 |
pangolin |
4.2 | 4.3.1 |
pangolin-data |
1.32 | |
pandas |
1.3.5 | 2.2.3 |
picard |
3.0.0 | 3.4.0 |
python |
3.9.5 | 3.13.2 |
quast |
5.2.0 | 5.3.0 |
regex |
2021.11.10 | 2024.11.6 |
r-base |
4.0.3 | 4.2.0 |
r-ggplot2 |
3.3.3 | 3.5.1 |
r-optparse |
1.6.6 | 1.7.5 |
r-reshape2 |
1.4.4 | 1.4.4 |
r-scales |
1.1.1 | 1.3.0 |
r-sys |
3.4 | 3.4.3 |
r-tidyverse |
1.3.0 | 1.3.2 |
r-viridis |
0.5.1 | 0.6.5 |
samtools |
1.16.1 | 1.22.1 |
scipy |
1.7.3 | 1.15.2 |
sed |
4.7 | 4.9 |
snakemake |
7.30.1 | 8.30.0 |
spades |
3.15.5 | 4.1.0 |
tabix |
1.11 | 1.21 |
Ubuntu |
20.04 | 24.04 |
unicycler |
0.4.8 | 0.5.1 |
vcflib |
1.0.3 | 1.0.14 |
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.
Full Changelog: 2.6.0...3.0.0
Contributors
heuermh, saramonzon, and 10 other contributors