v2.0.0 - Brazilian Escondidinho - [2024-09-05]
Breaking change
| Old parameter | New parameter |
|---|---|
annotation_bakta_db_localpath |
annotation_bakta_db |
arg_abricate_db |
arg_abricate_db_id |
arg_abricate_localdbdir |
arg_abricate_db |
arg_deeparg_data |
arg_deeparg_db |
arg_deeparg_data_version |
arg_deeparg_db_version |
arg_rgi_database |
arg_rgi_db |
bgc_antismash_databases |
bgc_antismash_db |
bgc_antismash_installationdirectory |
bgc_antismash_installdir |
bgc_deepbgc_database |
bgc_deepbgc_db |
save_databases |
save_db |
taxa_classification_mmseqs_databases_localpath |
taxa_classification_mmseqs_db |
taxa_classification_mmseqs_databases_id |
taxa_classification_mmseqs_db_id |
taxa_classification_mmseqs_databases_savetmp |
taxa_classification_mmseqs_db_savetmp |
amp_skip_hmmsearch |
amp_run_hmmsearch |
bgc_skip_hmmsearch |
bgc_run_hmmsearch |
- #343 Standardized the resulting workflow summary tables to always start with 'sample_id\tcontig_id\t..'. Reformatted the output of
hamronization/summarizemodule. (by @Darcy220606) - #411 Optimised hAMRonization input: only high-quality hits from fARGene output are reported. (by @jasmezz, @jfy133)
Added
- #322 Updated all modules: introduce environment.yml files. (by @jasmezz)
- #324 Removed separate DeepARG test profile because database download is now stable. (by @jasmezz)
- #332 & #327 Merged pipeline template of nf-core/tools version 2.12.1 (by @jfy133, @jasmezz)
- #338 Set
--metaparameter to default for Bakta, with singlemode optional. (by @jasmezz) - #343 Added contig taxonomic classification using MMseqs2. (by @Darcy220606)
- #358 Improved RGI databases handling, users can supply their own CARD now. (by @jasmezz)
- #375 Merged pipeline template of nf-core/tools version 2.14.1. (by @jfy133)
- #381 Added support for supplying pre-annotated sequences to the pipeline. (by @jfy133, @jasmezz)
- #382 Optimised BGC screening run time and prevent crashes due to too-short contigs by adding contig length filtering for BGC workflow only. (by @jfy133, @Darcy220606)
- #366 Added nf-test on pipeline level. (by @jfy133, @Darcy220606, @jasmezz)
- #403 Added antiSMASH parameters
--pfam2go,--rre, and--tfbs. (reported by @Darcy220606, added by @jasmezz) - #405 Added argNorm to ARG subworkflow. (by @Vedanth-Ramji)
Fixed
- #348 Updated samplesheet for pipeline tests to 'samplesheet_reduced.csv' with smaller datasets to reduce resource consumption. Updated prodigal module to fix pigz issue. Removed
tests/from.gitignore. (by @Darcy220606) - #362 Save annotations from bakta in subdirectories per sample. (by @jasmezz)
- #363 Removed warning from DeepBGC usage docs. (by @jasmezz)
- #365 Fixed AMRFinderPlus module and usage docs for manual database download. (by @jasmezz)
- #371 Fixed AMRFinderPlus parameter
arg_amrfinderplus_name. (by @m3hdad) - #377 Fixed an occasional RGI process failure when certain files not produced. (❤️ to @amizeranschi for reporting, fix by @amizeranschi & @jfy133)
- #386 Updated DeepBGC module to fix output file names, separate annotation step for all BGC tools, add warning if no BGCs found, fix MultiQC reporting of annotation workflow. (by @jfy133, @jasmezz)
- #393 & #397 Fixed a docker/singularity only error appearing when running with conda. (❤️ to @ewissel for reporting, fix by @jfy33 & @jasmezz)
- #391 Skip hmmmsearch by default to not crash pipeline if user provides no HMM files, updated docs. (by @jasmezz)
- #397 Removed deprecated AMPcombi module, fixed variable name in BGC workflow, updated minor parts in docs (usage, parameter schema). (by @jasmezz)
- #402 Fixed BGC length calculation for antiSMASH hits by comBGC. (by @jasmezz)
- #406 Fixed prediction tools not being executed if annotation workflow skipped. (by @jasmezz)
- #407 Fixed comBGC bug when parsing multiple antiSMASH files. (by @jasmezz)
- #409 Fixed argNorm overwriting its output for DeepARG. (by @jasmezz, @jfy133)
- #412 Improve all pre-run database download documentation. (by @jfy133)
Dependencies
| Tool | Previous version | New version |
|---|---|---|
| AMPcombi | 0.1.7 | 0.2.2 |
| AMPlify | 1.1.0 | 2.0.0 |
| AMRFinderPlus | 3.11.18 | 3.12.8 |
| antiSMASH | 6.1.1 | 7.1.0 |
| argNorm | NA | 0.5.0 |
| bioawk | 1.0 | NA |
| comBGC | 1.6.1 | 1.6.2 |
| DeepARG | 1.0.2 | 1.0.4 |
| DeepBGC | 0.1.30 | 0.1.31 |
| GECCO | 0.9.8 | 0.9.10 |
| hAMRonization | 1.1.1 | 1.1.4 |
| HMMER | 3.3.2 | 3.4 |
| MMSeqs | NA | 2:15.6f452 |
| MultiQC | 1.15 | 1.24 |
| Pyrodigal | 2.1.0 | 3.3.0 |
| RGI | 5.2.1 | 6.0.3 |
| seqkit | NA | 2.8.1 |
| tabix/htslib | 1.11 | 1.20 |
Deprecated
- #384 Deprecated AMPcombi and exchanged it with full suite of AMPcombi2 submodules. (by @Darcy220606)
- #382 Optimised BGC screening run time and prevent crashes due to too-short contigs by adding contig length filtering for BGC workflow only. Bioawk is replaced with seqkit. (by @jfy133, @Darcy220606)
Photo by Victória Galina under CC BY-NC 3.0 BR
Contributors
amizeranschi, jfy133, and 5 other contributors