nf-core/funcscan
(Meta-)genome screening for functional and natural product gene sequences
ampamrantibiotic-resistanceantimicrobial-peptidesantimicrobial-resistance-genesargassemblybgcbiosynthetic-gene-clusterscontigsfunctionmetagenomicsnatural-productsscreeningsecondary-metabolites
Version history
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
v1.1.6 - [2024-07-08]
Added
Fixed
- #396 Fixed bioawk overwriting input files. (❤️ to @Microbion for reporting, fix by @jfy133)
Dependencies
v1.1.5 - [2024-03-20]
Added
Fixed
- #346 Pinned version of nf-validation to 1.1.3
Dependencies
| Plugin | Previous | New version |
|---|---|---|
| Bakta | 1.8.2 | 1.9.3 |
| nf-validation | Latest | 1.1.3 |
Deprecated
v1.1.4 - [2023-11-07]
Added
Fixed
- #306 Added new parameter
annotation_prokka_retaincontigheadersto allow prokka to retain the original contig headers/locus tag. (by @darcy220606) - #307 Fixed stability of deepARG tests by using Zenodo copy of database (❤️ to Gustavo Arango and Liqing Zhang for uploading, fix by @jfy133)
- #310 Fixed error when supplying uncompressed input; added “fas” file extension for FASTA files. (by @tavareshugo)
- #311 Merged pipeline template of nf-core/tools version 2.10. (by @jasmezz)
Dependencies
| Tool | Previous version | New version |
|---|---|---|
| AMRFinderPlus | 3.10.42 | 3.11.18 |
| Bakta | 1.7.0 | 1.8.2 |
| MultiQC | 1.14 | 1.15 |
Deprecated
- FastQC
v1.1.3 - [2023-08-11]
Added
- #290 Merged pipeline template of nf-core/tools version 2.9, updated references. (by @jfy133)
- #285 Use nf-validation for samplesheet checking and added support for
fna.gzinput FASTA files. (by @louperelo, @mirpedrol, @jfy133) - #295 Add Prokka to MultiQC output. (by @louperelo)
Fixed
- #296 Fixed empty output when saving prodigal annotations. (reported by @louperelo, fix by @jasmezz)
- #297 Added check for empty annotation files prior going into screening. (❤️ to @alexhbnr for requesting, added by @jfy133)
- #299 Fixed pigz error with symlinks in Pyrodigal. (by @jasmezz)
- #300 Fixed wrong Pyrodigal channels being submitted to antiSMASH. (reported by Till Bayer, fix by @jasmezz)
- #302 Removed trouble-causing default parameters in json schema. (by @robsyme)
Dependencies
| Tool | Previous version | New version |
|---|---|---|
| comBGC | 0.6.0 | 0.6.1 |
| GECCO | 0.9.2 | 0.9.8 |
Deprecated
v1.1.2 - [2023-06-30]
Added
Fixed
- #279 Fix docker/podman registry definition for tower compatibility. (♥️ to @sunitj for reporting, fix by @adamrtalbot)
Dependencies
Deprecated
v1.1.1 - [2023-05-24]
Added
- #270 Merged pipeline template of nf-core/tools version 2.8 and updated modules accordingly. (by @jasmezz, @jfy133)
- #274 Update all modules: changed docker links according to the change of quay.io as default repository and Pyrodigal annotation output now zipped. (by @jasmezz)
- #275 Save DRAMP database in the common database directory if
--save_databasesis supplied. (by @jasmezz)
Fixed
- #272 Fix typo in Prokka output path in modules.config. (by @jasmezz)
- #273 Update Ampir module after input bugfix in module. (reported by @mathavanpu, fix by @louperelo)
- #276 Fix Pyrodigal parameters in modules.config. (by @jasmezz)
Dependencies
Deprecated
v1.1.0 - British Beans on Toast - [2023-04-27]
Added
- #238 Added dedicated DRAMP database downloading step for AMPcombi to prevent parallel downloads when no database provided by user. (by @jfy133)
- #235 Added parameter
annotation_bakta_db_downloadtypeto be able to switch between downloading either full (33.1 GB) or light (1.3 GB excluding UPS, IPS, PSC, see parameter description) versions of the Bakta database. (by @jasmezz) - #249 Added bakta annotation to CI tests. (by @jasmezz)
- #251 Added annotation tool: Pyrodigal. (by @jasmezz)
- #252 Added a new parameter
-arg_rgi_savejsonthat saves the file<samplename>.jsonin the RGI directory. The default ouput for RGI is now only<samplename>.txt. (by @darcy220606) - #253 Updated Prodigal to have compressed output files. (by @jasmezz)
- #262 Added comBGC function to screen whole directory of antiSMASH output (one subfolder per sample). (by @jasmezz)
- #263 Removed
AMPlifyfrom test_full.config. (by @jasmezz) - #266 Updated README.md with Pyrodigal. (by @jasmezz)
Fixed
- #243 Compress the ampcombi_complete_summary.csv in the output directory. (by @louperelo)
- #237 Reactivate DeepARG automatic database downloading and CI tests as server is now back up. (by @jfy133)
- #235 Improved annotation speed by switching off pipeline-irrelevant Bakta annotation steps by default. (by @jasmezz)
- #235 Renamed parameter
annotation_bakta_dbtoannotation_bakta_db_localpath. (by @jasmezz) - #242 Fixed MACREL ‘.faa’ issue that was generated when it was run on its own and upgraded MACREL from version
1.1.0to1.2.0(by @Darcy220606) - #248 Applied best-practice
error("message")to all (sub)workflow files. (by @jasmezz) - #254 Further resource optimisation based on feedback from ‘real world’ datasets. (ongoing, reported by @alexhbnr and @Darcy220606, fix by @jfy133)
- #266 Fixed wrong process name in base.config. (reported by @Darcy220606, fix by @jasmezz)
Dependencies
| Tool | Previous version | New version |
|---|---|---|
| Bakta | 1.6.1 | 1.7.0 |
Deprecated
Photo by Jon Chan under CC BY-SA 2.0
v1.0.1 - [2023-02-27]
Added
- #229 Added pipeline DOI to
WorkflowMain.groovyto display citation info when executing the pipeline. (by @jasmezz)
Fixed
- #227 Removed a header check in the
check_samplesheet.pyscript that was producing false negatives. Presence of required columns is still validated. (by @Midnighter) - #228 Improved database downloading guidance to emphasise it is recommended to let nf-core/funcscan do the downloading on a first run, rather than manually downloading yourself. (reported by @alexhbnr, fixed by @jfy133)
Dependencies
Deprecated
v1.0.0 - German Rollmops - [2023-02-15]
Initial release of nf-core/funcscan, created with the nf-core template.
Added
- Added annotation tools (Prokka, Prodigal, Bakta).
- Added AMP screening workflow (tools: Macrel, AMPlify, ampir, hmmsearch).
- Added ARG screening workflow (tools: ABRicate, AMRFinderPlus, DeepARG, fARGene).
- Added BGC screening workflow (tools: antiSMASH, DeepBGC, GECCO, hmmsearch).
- Added workflow summary tools (tools: hAMRonization, AMPcombi, comBGC).
Fixed
Dependencies
Deprecated
Photo by Ra Boe under CC BY-SA 2.5
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